Generation of phased read-sets for genome assembly and haplotype phasing

ABSTRACT

Disclosed herein are methods, compositions and systems that facilitate accurate phasing of sequence data such as genomic sequence data through the segmentation and rearrangement of nucleic acid molecules in such a way as to preserve individual molecules&#39; phase or physical linkage information. This is variously accomplished by binding molecules independent of their phosphodiester backbones, cleaving the molecules, ligating, and sequencing the molecules through long-read sequencing technology to recover segment sequence information spanning at least more than one segment.

CROSS-REFERENCE

This application is a continuation of U.S. patent application Ser. No.16/078,741, filed Aug. 22, 2018, which is national stage entry ofInternational Application No. PCT/US17/19099, filed Feb. 23, 2017, whichclaims the benefit of U.S. Provisional Application No. 62/298,906, filedFeb. 23, 2016, which is hereby explicitly incorporated by reference inits entirety, and this application also claims the benefit of U.S.Provisional Application No. 62/298,966, filed Feb. 23, 2016, which ishereby explicitly incorporated by reference in its entirety, and thisapplication also claims the benefit of U.S. Provisional Application No.62/305,957, filed Mar. 9, 2016, which is hereby explicitly incorporatedby reference in its entirety.

BACKGROUND

It remains difficult in theory and in practice to determine haplotypephase information of complex DNA samples, such as those having diploidor polyploid genomes, or those comprising substantial amounts ofrepetitive or identical sequence. Difficulties arise from loci ofinterest being separated by highly repetitive regions or by longstretches of identical sequence, such that standard assembly of readinformation is insufficient to assign phase information to alleles at alocus.

SUMMARY

Disclosed herein are methods, compositions and systems related to theaccurate phasing of nucleic acid sequence data through the generationand sequencing, such as long-read sequencing, of segmentally rearrangednucleic acid molecules such as chromosomes.

Disclosed herein are methods of generating long-distance phaseinformation from a first DNA molecule, comprising a) providing a firstDNA molecule having a first segment and a second segment, wherein thefirst segment and the second segment are not adjacent on the first DNAmolecule; b) contacting the first DNA molecule to a DNA binding moietysuch that the first segment and the second segment are bound to the DNAbinding moiety independent of a common phosphodiester backbone of thefirst DNA molecule; c) cleaving the first DNA molecule such that thefirst segment and the second segment are not joined by a commonphosphodiester backbone; d) attaching the first segment to the secondsegment via a phosphodiester bond to form a reassembled first DNAmolecule; and e) sequencing at least 4 kb of consecutive sequence of thereassembled first DNA molecule comprising a junction between the firstsegment and the second segment in a single sequencing read, whereinfirst segment sequence and second segment sequence representlong-distance phase information from a first DNA molecule. In someaspects the DNA binding moiety comprises a plurality of DNA-bindingmolecules, such as DNA-binding proteins. In some aspects the populationof DNA-binding proteins comprises nuclear proteins broadly, nucleosomes,or in some cases, more specifically histones. In some aspects contactingthe first DNA molecule to a plurality of DNA-binding moieties comprisescontacting to a population of DNA-binding nanoparticles. Often, thefirst DNA molecule has a third segment not adjacent on the first DNAmolecule to the first segment or the second segment, wherein thecontacting in (b) is conducted such that the third segment is bound tothe DNA binding moiety independent of the common phosphodiester backboneof the first DNA molecule, wherein the cleaving in (c) is conducted suchthat the third segment is not joined by a common phosphodiester backboneto the first segment and the second segment, wherein the attachingcomprises attaching the third segment to the second segment via aphosphodiester bond to form the reassembled first DNA molecule, andwherein the consecutive sequence sequenced in (e) comprises a junctionbetween the second segment and the third segment in a single sequencingread. The method often comprises contacting the first DNA molecule to across-linking agent, such as formaldehyde. In some aspects the DNAbinding moiety is bound to a surface comprising a plurality of DNAbinding moieties. In some aspects the DNA binding moiety is bound to asolid framework comprising a bead. In some aspects cleaving the firstDNA molecule comprises contacting to a restriction endonuclease such asa nonspecific endonuclease, a tagmentation enzyme, or a transposase. Insome aspects cleaving the first DNA molecule comprises shearing thefirst molecule. Optionally, the method comprises adding a tag to atleast one exposed end. Exemplary tags comprise a labeled base, amethylated base, a biotinylated base, uridine, or any other noncanonicalbase. In some aspects the tag generates a blunt ended exposed end. Insome aspects the method comprises adding at least one base to a recessedstrand of a first segment sticky end. In some aspects the methodcomprises adding a linker oligo comprising an overhang that anneals tothe first segment sticky end. In some aspects the linker oligo comprisesan overhang that anneals to the first segment sticky end and an overhangthat anneals to the second segment sticky end. In some aspects thelinker oligo does not comprise two 5′ phosphate moieties. In someaspects attaching comprises ligating. In some aspects attachingcomprises DNA single strand nick repair. In some aspects the firstsegment and the second segment are separated by at least 10 kb on thefirst DNA molecule prior to cleaving the first DNA molecule. In someaspects the first segment and the second segment are separated by atleast 15 kb on the first DNA molecule prior to cleaving the first DNAmolecule. In some aspects the first segment and the second segment areseparated by at least 30 kb on the first DNA molecule prior to cleavingthe first DNA molecule. In some aspects the first segment and the secondsegment are separated by at least 50 kb on the first DNA molecule priorto cleaving the first DNA molecule. In some aspects the first segmentand the second segment are separated by at least 100 kb on the first DNAmolecule prior to cleaving the first DNA molecule. In some aspects thesequencing comprises single molecule long read sequencing. In someaspects the long read sequencing comprises a read of at least 5 kb. Insome aspects the long read sequencing comprises a read of at least 10kb. In some aspects the first reassembled DNA molecule comprises ahairpin moiety linking a 5′ end to a 3′ end at one end of the first DNAmolecule. In some aspects the method comprises sequencing a secondreassembled version of the first DNA molecule. In some aspects the firstsegment and the second segment are each at least 500 bp. In some aspectsthe first segment, the second segment, and the third segment are each atleast 500 bp.

Disclosed herein are methods of genome assembly comprising: a) obtaininga first DNA molecule complexed to a structure; b) cleaving the first DNAmolecule to form a first exposed end and a second exposed end, whereinthe first exposed end and the second exposed end were not adjacent onthe molecule prior to said cleaving; c) cleaving the first DNA moleculeto form a third exposed end and a fourth exposed end, wherein the thirdexposed end and the fourth exposed end were not adjacent on the moleculeprior to said cleaving; d) attaching said first exposed end and saidsecond exposed end to form a first junction; e) attaching said thirdexposed end and said fourth exposed end to form a second junction; f)sequencing across said first junction and said second junction in asingle sequencing read; g) mapping sequence on a first side of saidfirst junction to a first contig of said plurality of contigs; h)mapping sequence on a second side of said first junction to a secondcontig of said plurality of contigs; i) mapping sequence on a first sideof said second junction to a second contig of said plurality of contigs;j) mapping sequence on a second side of said second junction to a thirdcontig of said plurality of contigs; and k) assigning said first contig,said second contig, and said third contig to a common phase of a genomeassembly. In some aspects, said plurality of contigs are generated fromshotgun sequence data. In some aspects said plurality of contigs aregenerated from single molecule long read data. In some aspects, saidsingle molecule long read data comprises said plurality of contigs. Insome aspects, said plurality of contigs is concurrently obtained throughsequencing across said first junction and said second junction. In someaspects, sequencing across said marker oligo comprises sequencing atleast 10 kb. In some aspects, said structure comprises a population ofDNA binding moieties bound to the first DNA molecule to formreconstituted chromatin. In some aspects, said reconstituted chromatinis contacted to a crosslinking agent. In some aspects, said crosslinkingagent comprises formaldehyde. In some aspects, said population of DNAbinding moieties comprises histones. In some aspects, said population ofDNA binding moieties comprises nanoparticles. In some aspects, saidstructure comprises native chromatin. In some aspects, the first exposedend and the second exposed end are separated by at least 10 kb on thefirst DNA molecule prior to cleaving the first DNA molecule. In someaspects, the first exposed end and the second exposed end are separatedby at least 15 kb on the first DNA molecule prior to cleaving the firstDNA molecule. In some aspects, the first exposed end and the secondexposed end are separated by at least 30 kb on the first DNA moleculeprior to cleaving the first DNA molecule. In some aspects, the firstexposed end and the second exposed end are separated by at least 50 kbon the first DNA molecule prior to cleaving the first DNA molecule. Insome aspects, the first exposed end and the second exposed end areseparated by at least 100 kb on the first DNA molecule prior to cleavingthe first DNA molecule. In some aspects, the method comprises sequencinga second copy of the first DNA molecule.

Disclosed herein are rearranged nucleic acid molecules of at least 5 kbcomprising a) a first segment; b) a second segment; and c) a thirdsegment; said first segment and said second segment being joined at afirst junction; and said second segment and said third segment beingjoined at a second junction; wherein said first segment, said secondsegment and said third segment exist in phase separated by at least 10kb in an unrearranged nucleic acid molecule, and wherein at least 70% ofsaid rearranged nucleic acid molecule maps to said common unrearrangednucleic acid molecule. In some aspects, the first segment, the secondsegment and the third segment comprise separate genomic nucleic acidsequence from a common nucleic acid molecule of a genome. In someaspects, the first segment, the second segment and the third segmentexist in a common molecule in the genome in an order that is rearrangedin the rearranged nucleic acid. In some aspects, said nucleic acidmolecule is at least 30 kb in length. In some aspects, said nucleic acidcomprises a hairpin loop at a double-stranded terminal end, so that themolecule comprises a single strand comprising a 30 kb inverted repeat.In some aspects, said nucleic acid is a double-stranded circularmolecule. In some aspects, at least 80% of said rearranged nucleic acidmolecule maps to said common unrearranged nucleic acid molecule. In someaspects, at least 85% of said rearranged nucleic acid molecule maps tosaid common unrearranged nucleic acid molecule. In some aspects, atleast 90% of said rearranged nucleic acid molecule maps to said commonunrearranged nucleic acid molecule. In some aspects, at least 95% ofsaid rearranged nucleic acid molecule maps to said common unrearrangednucleic acid molecule. In some aspects, at least 99% of said rearrangednucleic acid molecule maps to said common unrearranged nucleic acidmolecule. In some aspects, at least 80% of segments of said rearrangednucleic acid molecule maps to said common unrearranged nucleic acidmolecule. In some aspects, at least 85% of segments of said rearrangednucleic acid molecule maps to said common unrearranged nucleic acidmolecule. In some aspects, at least 90% of segments of said rearrangednucleic acid molecule maps to said common unrearranged nucleic acidmolecule. In some aspects, at least 95% of segments of said rearrangednucleic acid molecule maps to said common unrearranged nucleic acidmolecule. In some aspects, at least 99% of segments of said rearrangednucleic acid molecule maps to said common unrearranged nucleic acidmolecule. In some aspects, the rearranged nucleic acid is generated bysteps of any of the methods disclosed herein.

Disclosed herein are methods of generating a phased sequence of a samplenucleic acid molecule comprising a) generating a first rearrangednucleic acid molecule as disclosed herein from the sample nucleic acidmolecule; b) generating a second rearranged nucleic acid molecule asdisclosed herein from the sample nucleic acid molecule; and c)sequencing the first rearranged nucleic acid molecule and the secondrearranged nucleic acid molecule; wherein the first rearranged nucleicacid molecule and the second rearranged nucleic acid molecule areindependently generated

Disclosed herein are methods of generating a phased sequence of a samplenucleic acid molecule comprising a) sequencing a first rearrangednucleic acid molecule as disclosed herein from the sample nucleic acidmolecule; b) sequencing a second rearranged nucleic acid molecule asdisclosed herein from the sample nucleic acid molecule; wherein thefirst rearranged nucleic acid molecule and the second rearranged nucleicacid molecule are independently generated; and c) assembling sequence ofthe first rearranged nucleic acid molecule as disclosed herein and thesecond rearranged nucleic acid molecule as disclosed herein such that anassembled sequence is an unrearranged phased sequence of a samplenucleic acid molecule. In some aspects, sequencing a first rearrangednucleic acid molecule comprises generating a sequence read of at least 1kb. In some aspects, sequencing a first rearranged nucleic acid moleculecomprises generating a sequence read of at least 2 kb. In some aspects,sequencing a first rearranged nucleic acid molecule comprises generatinga sequence read of at least 5 kb. In some aspects, the method comprisesassigning at least 70% of said first rearranged molecule to a commonphase of a single genomic molecule. In some aspects, the methodcomprises assigning at least 70% of said second rearranged molecule to acommon phase of a single genomic molecule. In some aspects, the methodcomprises assigning at least 80% of said first rearranged molecule to acommon phase of a single genomic molecule. In some aspects, the methodcomprises assigning at least 80% of said second rearranged molecule to acommon phase of a single genomic molecule. In some aspects, the methodcomprises assigning at least 90% of said first rearranged molecule to acommon phase of a single genomic molecule. In some aspects, the methodcomprises assigning at least 90% of said second rearranged molecule to acommon phase of a single genomic molecule. In some aspects, the methodcomprises assigning at least 95% of said first rearranged molecule to acommon phase of a single genomic molecule. In some aspects, the methodcomprises assigning at least 95% of said second rearranged molecule to acommon phase of a single genomic molecule.

Disclosed herein are methods of phasing long-read sequence datacomprising a) obtaining sequence data from any nucleic acid sampledisclosed herein; b) obtaining long-read sequence data from anyrearranged nucleic acid as disclosed herein; c) mapping the long-readsequence data from the rearranged nucleic acid to the sequence data fromthe nucleic acid sample; and d) assigning to a common phase the sequencedata from the nucleic acid sample mapped to by the long-read sequencedata from the rearranged nucleic acid.

Disclosed herein are methods of providing phase information to a nucleicacid dataset generated from a nucleic acid sample by a DNA sequencingtechnology, comprising a) obtaining a nucleic acid of said nucleic acidsample having a first segment and a second segment separated by adistance greater than a read length of the DNA sequencing technology; b)shuffling the nucleic acid such that the first segment and the secondsegment are separated by a distance less than a read length of the DNAsequencing technology; c) sequencing the shuffled nucleic acid using theDNA sequencing technology such that the first segment and the secondsegment appear in a single read of the DNA sequencing technology; and d)assigning sequence reads of the data set comprising first segmentsequence and sequence reads of the data set comprising second segmentsequence to a common phase. In some aspects, the DNA sequencingtechnology generates reads having a read length of at least 10 kb. Insome aspects, shuffling comprises performing steps of any methodsdisclosed herein. In some aspects, the first segment and the secondsegment are separated by a linker oligo that marks a segment end.

Disclosed herein are nucleic acid sequence databases comprising sequenceinformation obtained from a plurality of molecules as disclosed herein,wherein sequence information corresponding to molecules having less than70% of their segments map to a common scaffold is excluded from at leastone analysis.

Disclosed herein are nucleic acid sequence databases comprising sequenceinformation obtained from a plurality of molecules as disclosed herein,wherein sequence information corresponding to molecules having less than70% of their sequence information map to a common scaffold is excludedfrom at least one analysis.

Disclosed herein are methods of phasing long-read sequence datacomprising a) obtaining sequence data from any nucleic acid sampledisclosed herein; b) obtaining long-read sequence data from therearranged nucleic acid of any rearranged nucleic acid disclosed herein;c) mapping the first segment, the second segment and the third segmentof the rearranged nucleic acid to the sequence data from the nucleicacid sample to the nucleic acid sample sequence data; and d) when atleast two segments map to a common scaffold, assigning sequencevariation of said segments to a common phase. In some aspects, the firstsegment comprises a single nucleotide polymorphism relative to thesequence data from the nucleic acid sample. In some aspects, the firstsegment comprises an insertion relative to the sequence data from thenucleic acid sample. In some aspects, the first segment comprises adeletion relative to the sequence data from the nucleic acid sample. Insome aspects, the method comprises assigning a first set of segmentsmapping to a first common scaffold to a common phase of the first commonscaffold, and assigning a second set of segments mapping to a secondcommon scaffold to a common phase of the second common scaffold.

Disclosed herein are nucleic acid sequence libraries of a nucleic acidsample, said nucleic acid sequence library comprising a population ofnucleic acid sequence reads having an average read length, at least oneof said reads comprising at least 500 bases of a first nucleic acidsegment and at least 500 bases of a second nucleic acid segment, whereinsaid first nucleic acid segment and said second nucleic acid segment arefound in phase separated by a distance greater than said average readlength on a common molecule of said nucleic acid sample. In someaspects, said first nucleic acid segment and said second nucleic acidsegment are found in phase separated by a distance greater than 10 kb.In some aspects, said first nucleic acid segment and said second nucleicacid segment are found in phase separated by a distance greater than 20kb. In some aspects, said first nucleic acid segment and said secondnucleic acid segment are found in phase separated by a distance greaterthan 50 kb. In some aspects, said first nucleic acid segment and saidsecond nucleic acid segment are found in phase separated by a distancegreater than 100 kb. In some aspects, at least one of said readscomprises at least 1 kb of a first nucleic acid segment. In someaspects, at least one of said reads comprises at least 5 kb of a firstnucleic acid segment. In some aspects, at least one of said readscomprises at least 10 kb of a first nucleic acid segment. In someaspects, at least one of said reads comprises at least 20 kb of a firstnucleic acid segment. In some aspects, at least one of said readscomprises at least 50 kb of a first nucleic acid segment. In someaspects, nucleic acid sequence library comprises at least 80% of saidnucleic acid sample. In some aspects, nucleic acid sequence librarycomprises at least 85% of said nucleic acid sample. In some aspects,nucleic acid sequence library comprises at least 90% of said nucleicacid sample. In some aspects, nucleic acid sequence library comprises atleast 95% of said nucleic acid sample. In some aspects, nucleic acidsequence library comprises at least 99% of said nucleic acid sample. Insome aspects, nucleic acid sequence library comprises at least 99.9% ofsaid nucleic acid sample.

Disclosed herein are nucleic acid sequence libraries of a nucleic acidsample, said nucleic acid sequence library comprising a population ofnucleic acid sequence reads having a mean length of at least 1 kb, saidreads independently comprising at least 300 bases of sequence from twoseparate in phase regions of the nucleic acid sample, said two separatein phase regions separated by a distance greater than 10 kb in thenucleic acid sample. In some aspects, said reads independently compriseat least 500 bases of sequence from two separate in phase regions of thenucleic acid sample. In some aspects, said reads independently compriseat least 1 kb of sequence from two separate in phase regions of thenucleic acid sample. In some aspects, said reads independently compriseat least 2 kb of sequence from two separate in phase regions of thenucleic acid sample. In some aspects, said reads independently compriseat least 5 kb of sequence from two separate in phase regions of thenucleic acid sample. In some aspects, said reads independently compriseat least 10 kb of sequence from two separate in phase regions of thenucleic acid sample. In some aspects, said two separate in phase regionsare separated by a distance greater than 20 kb in the nucleic acidsample. In some aspects, said two separate in phase regions areseparated by a distance greater than 30 kb in the nucleic acid sample Insome aspects, said two separate in phase regions are separated by adistance greater than 50 kb in the nucleic acid sample in at least 1% ofthe reads. In some aspects, said two separate in phase regions areseparated by a distance greater than 100 kb in the nucleic acid samplein at least 1% of the reads. In some aspects, nucleic acid sequencelibrary comprises at least 80% of said nucleic acid sample. In someaspects, nucleic acid sequence library comprises at least 85% of saidnucleic acid sample. In some aspects, nucleic acid sequence librarycomprises at least 90% of said nucleic acid sample. In some aspects,nucleic acid sequence library comprises at least 95% of said nucleicacid sample. In some aspects, nucleic acid sequence library comprises atleast 99% of said nucleic acid sample. In some aspects, nucleic acidsequence library comprises at least 99.9% of said nucleic acid sample.

Disclosed herein are nucleic acid libraries generated from a nucleicacid sample, wherein at least 80% of nucleic acid sequence of thenucleic acid sample is represented in the nucleic acid library; and inphase sequence segments of the nucleic acid sample are rearranged suchthat at least one distantly positioned pair of in phase segments of thenucleic acid sample is read in a single sequence read; such thatsequencing said library concurrently generates contig informationspanning at least 80% of the nucleic acid sample, and phase informationsufficient to order and orient said contig information to generate aphased sequence of said nucleic acid sample. In some aspects, at least90% of nucleic acid sequence of the nucleic acid sample is representedin the nucleic acid library. In some aspects, at least 95% of nucleicacid sequence of the nucleic acid sample is represented in the nucleicacid library. In some aspects, at least 99% of nucleic acid sequence ofthe nucleic acid sample is represented in the nucleic acid library. Insome aspects, said 80% of nucleic acid sequence of the nucleic acidsample is obtained from no more than 100,000 library constituents. Insome aspects, said 80% of nucleic acid sequence of the nucleic acidsample is obtained from no more than 10,000 library constituents. Insome aspects, said 80% of nucleic acid sequence of the nucleic acidsample is obtained from no more than 1,000 library constituents. In someaspects, said 80% of nucleic acid sequence of the nucleic acid sample isobtained from no more than 500 library constituents. In some aspects,the sample is a genomic sample. In some aspects, the sample is aeukaryotic genomic sample. In some aspects, the sample is a plantgenomic sample. In some aspects, the sample is an animal genomic sample.In some aspects, the sample is a mammalian genomic sample. In someaspects, the sample is a unicellular eukaryotic genomic sample. In someaspects, the sample is a human genomic sample. In some aspects, thenucleic acid library is not barcoded to preserve phase information. Insome aspects, a read of said library comprises at least 1 kb of sequencefrom a first region and at least 100 bases of sequence from a secondregion in phase the first region and separated by greater than 50 kbfrom the first region in the sample.

Disclosed herein are methods of configuring a nucleic acid molecule forsequencing on a sequencing device, wherein the nucleic acid moleculecomprises at least 100 kb of sequence, and wherein said at least 100 kbof sequence comprises a first segment and a second segment separated bya length greater than a read length of the sequencing device, comprisingchanging a relative position of the first segment relative to the secondsegment of the nucleic acid molecule, such that the first segment andthe segment are separated by less than the read length of the sequencingdevice; wherein phase information for the first segment and the secondsegment is maintained; and wherein no more than 10% of the nucleic acidmolecule is deleted. In some aspects, the method comprises generating aread spanning at least part of the first segment and the second segment.In some aspects, the method comprises assigning the first segment andthe second segment to a common phase of a sequence of the nucleic acidmolecule. In some aspects, no more than 5% of the nucleic acid moleculeis deleted. In some aspects, no more than 1% of the nucleic acidmolecule is deleted. In some aspects, the first segment and the secondsegment are separated by at least 10 kb in the nucleic acid moleculeprior to configuring. In some aspects, the first segment and the secondsegment are separated by at least 50 kb in the nucleic acid moleculeprior to configuring. In some aspects, the first segment and the secondsegment are separated by a junction marker following said configuring.In some aspects, the method comprises attaching a stem loop at an end ofthe nucleic acid, thereby converting the molecule to a single strand. Insome aspects, the method comprises circularizing the nucleic acidmolecule. In some aspects, the method comprises attaching the nucleicacid molecule to a DNA polymerase. In some aspects, the method comprisesbinding the nucleic acid molecule such that the first segment and thesecond segment are held together independent of a phosphodiesterbackbone; cleaving a phosphodiester backbone between the first segmentand the second segment at at least two positions; and reattaching thefirst segment to the second segment, such that the first segment and thesecond segment are separated by less than a read length of thesequencing device. In some aspects, said cleaving and said reattachingdoes not result in loss of sequence information form said nucleic acidmolecule.

Disclosed herein are methods of generating long-distance phaseinformation from a first nucleic acid molecule, comprising: a) providinga sample comprising a first nucleic acid molecule having a firstsegment, a second segment, and a third segment, wherein none of thefirst segment, the second segment, and the third segment are adjacent onthe first nucleic acid molecule, wherein the first nucleic acid moleculeis contacted to a framework such that the first segment, the secondsegment, and the third segment are bound to the framework independent ofa common phosphodiester backbone of the first nucleic acid molecule; b)cleaving the first nucleic acid molecule such that the first segment,the second segment, and the third segment are not joined by a commonphosphodiester backbone; c) connecting the first segment to the secondsegment and connecting the second segment to the third segment; and d)sequencing a first portion of the first nucleic acid molecule comprisingthe first segment, the second segment, and the third segment, therebygenerating first segment sequence information, second segment sequenceinformation, and third segment sequence information, wherein the firstsegment sequence information, the second segment sequence information,and the third segment sequence information provide long-distance phaseinformation about the first nucleic acid molecule. In some aspects, theframework comprises reconstituted chromatin. In some aspects, theframework comprises native chromatin. In some aspects, the cleaving isconducted with a restriction enzyme. In some aspects, the cleaving isconducted with fragmentase. In some aspects, the method comprises, priorto the sequencing, removing from the sample a second portion of thefirst nucleic acid molecule comprising at most two segments. In someaspects, the method comprises assembling a sequence of the first nucleicacid molecule using the first segment sequence information, the secondsegment sequence information, and the third segment sequenceinformation.

Disclosed herein are methods of sequencing a nucleic acid molecule,comprising: a) obtaining a first nucleic acid molecule comprising afirst segment, a second segment and a third segment sharing a commonphosphodiester backbone, wherein none of said first segment, secondsegment and third segment are adjacent on said first nucleic acidmolecule; b) partitioning said nucleic acid molecule such that saidfirst segment, second segment and third segment are associatedindependent of their common phosphodiester backbone; c) cleaving saidnucleic acid molecule to generate fragments such that there is nocontinuous phosphodiester backbone linking the first segment, secondsegment and third segment; d) ligating said fragments such that saidfirst segment, second segment and third segment are consecutive on arearranged nucleic acid molecule sharing a common phosphodiesterbackbone; and e) sequencing at least a portion of said rearrangednucleic acid molecule such that at least 5,000 bases of said rearrangednucleic acid molecule are sequenced in a single read. In some aspects,partitioning comprises contacting said nucleic acid molecule to abinding moiety such that said first segment, second segment and thirdsegment are bound in a common complex independent of their commonphosphodiester backbone. In some aspects, contacting the nucleic acidmolecule to a plurality of DNA-binding molecules comprises contacting toa population of DNA-binding proteins. In some aspects, the population ofDNA-binding proteins comprises nuclear proteins. In some aspects, thepopulation of DNA-binding proteins comprises nucleosomes. In someaspects, the population of DNA-binding proteins comprises histones. Insome aspects, contacting the nucleic acid molecule to a plurality ofDNA-binding moieties comprises contacting to a population of DNA-bindingnanoparticles. In some aspects, cleaving the nucleic acid moleculecomprises contacting to a restriction endonuclease. In some aspects,cleaving the nucleic acid molecule comprises contacting to a nonspecificendonuclease. In some aspects, cleaving the nucleic acid moleculecomprises contacting to a tagmentation enzyme. In some aspects, cleavingthe nucleic acid molecule comprises contacting to a transposase. In someaspects, cleaving the nucleic acid molecule comprises shearing the firstmolecule. In some aspects, partitioning comprises separating saidnucleic acid molecule from other nucleic acid molecules of a sample. Insome aspects, partitioning comprises diluting said nucleic acid sample.In some aspects, partitioning comprises distributing said nucleic acidmolecule into a microdroplet of an emulsion.

Disclosed herein are nucleic acid molecules representative of genomicphase information of an organisms's genome, said nucleic acid moleculecomprising at least 20 kb of nucleic acid sequence information that mapsto a single genomic molecule, wherein said sequence informationcomprises segments rearranged relative to their position in the genomicmolecule, and wherein at least 70% of sequence information that uniquelymaps to said organism's genome maps to a single genomic molecule. Insome aspects, the nucleic acid molecule comprises at least 20 segments.In some aspects, said segments are not adjacent in said organism'sgenome.

Disclosed herein are nucleic acid libraries comprising at least 100nucleic acid molecule constituents of at least 20 kb, whereinconstituents comprise rearranged segments of an organism's genome;wherein at least 70% of uniquely mapping segments from a libraryconstituent map to a common genomic molecule; and wherein constituentsare not bound to nucleic acid binding moieties.

Disclosed herein are nucleic acid datasets comprising sequencescorresponding to at least 100 nucleic acid molecule constituents of atleast 20 kb, wherein constituents comprise at least 5 rearrangedsegments of an organism's genome, and wherein constituents for whichless than 70% of said rearranged segments map to a common scaffold areexcluded from a downstream analysis.

Disclosed herein are nucleic acid datasets comprising sequencescorresponding to at least 100 nucleic acid molecule constituents of atleast 20 kb, wherein constituents comprise at least 5 rearrangedsegments of an organism's genome, and wherein constituents for whichless than 70% of said sequence uniquely maps to a common scaffold areexcluded from a downstream analysis.

BRIEF DESCRIPTION OF THE DRAWINGS

Novel features of the disclosure are set forth with particularity in theappended claims and in summary and detailed descriptions herein. Abetter understanding of the features and advantages of the disclosurewill be obtained by reference to the following detailed description thatsets forth illustrative embodiments, in which the principles of thedisclosure are utilized, and the accompanying drawings of which:

FIG. 1 depicts a digested reconstituted chromatin aggregate with manyfree ends with single-stranded overhangs that are hybridizationcompatible with all other free ends.

FIG. 2 depicts the digested reconstituted chromatin aggregate of FIG. 1with a single base filled-in, making each single-stranded overhangincompatible for re-annealing and re-ligation.

FIG. 3 depicts the partially filled-in digested reconstituted chromatinaggregate of FIG. 2 ligated with punctuation oligonucleotides compatiblewith the modified free ends of the reconstituted aggregate.

FIG. 4 depicts a punctuated DNA molecule resulting from the ligationproduct of FIG. 3 followed by release from the DNA-binding proteins.Each genomic segment is delineated by the punctuation oligonucleotidewhich is identifiable by its known sequence. The genomic segments allrepresent some region of the input molecule in that startingreconstituted chromatin aggregate. Thus, the reads in this set arehaplotype phased and can be used for assembly or haplotype phasereconstruction.

FIG. 5 depicts concatemer generation of Chicago pairs. In the top panel,Chicago read pairs are generated by ligating biotinylated ends ofdigested reconstituted chromatin aggregates together (such as the endsin FIG. 1 if they were biotinylated and cleaved following ligation).These molecules are captured on streptavidin-coated beads. Then,amplification adapters are added. All molecules are bulk amplified andcollected from the streptavidin-bead supernatant. Finally, thesemolecules are bulk ligated together to generate long molecules which canbe read using a long-read sequencing technology. The embedded read pairsare identifiable via the amplification adapters.

FIG. 6 depicts barcoding a punctuated molecule, such as the moleculedepicted in FIG. 4 or the long molecule generated in FIG. 5. First,delivery of barcoded oligonucleotides that are composed of a barcode anda reverse complement to the punctuation oligonucleotide is done. Then,these barcoded oligonucleotides are extended such that the productcontains the barcode, the punctuation sequence and some genomicsequence.

FIG. 7 depicts a gel electrophoresis analysis of two samples, before theligation step (‘BF’) and after the ligation step (‘AF’), demonstratingsuccessful ligation to form long rearranged molecules.

FIG. 8 presents data obtained from a rearranged genomic library.

FIG. 9A depicts frequency distributions of distance spanned by readssegregated into 10 kb bins.

FIG. 9B depicts frequency distributions of distance spanned by readssegregated into 1 kb bins.

FIG. 10 depicts a computer system for implementation of the disclosure.

DETAILED DESCRIPTION

Disclosed herein are methods for generating read sets, including phasedread-sets, for applications including genome assembly and haplotypephasing, using long-read or short-read sequencing technologies. Nucleicacid molecules can be bound (e.g., in a chromatin structure), cleaved toexpose internal ends, re-attached at junctions to other exposed ends,freed from binding, and sequenced. This technique can produce nucleicacid molecules comprising multiple sequence segments. The multiplesequence segments within a nucleic acid molecule can have phaseinformation preserved while being rearranged relative to their naturalor starting position and orientation. Sequence segments on either sideof a junction can be confidently considered to come from the same phaseof a sample nucleic acid molecule.

Nucleic acid molecules, including high molecular weight DNA, can bebound or immobilized on at least one nucleic acid binding moiety. Forexample, DNA assembled into in vitro chromatin aggregates and fixed withformaldehyde treatment are consistent with methods herein. Nucleic acidbinding or immobilizing approaches include, but are not limited to, invitro or reconstituted chromatin assembly, native chromatin, DNA-bindingprotein aggregates, nanoparticles, DNA-binding beads or beads coatedusing a DNA-binding substance, polymers, synthetic DNA-binding moleculesor other solid or substantially solid affinity molecules. In some cases,the beads are solid phase reversible immobilization (SPRI) beads (e.g.,beads with negatively charged carboxyl groups such as Beckman-CoulterAgencourt AMPure XP beads).

Nucleic acids bound to a nucleic acid binding moiety such as thosedescribed herein can be held such that a nucleic acid molecule having afirst segment and a second segment separated on the nucleic acidmolecule by a distance greater than a read distance on a sequencingdevice (10 kb, 50 kb, 100 kb or greater, for example) are bound togetherindependent of their common phosphodiester bonds. Upon cleavage of sucha bound nucleic acid molecule, exposed ends of the first segment and thesecond segment may ligate to one another. In some cases, the nucleicacid molecules are bound at a concentration such that there is little orno overlap between bound nucleic acid molecules on a solid surface, suchthat exposed internal ends of cleaved molecules are likely to re-ligateor become reattached only to exposed ends from other segments that werein phase on a common nucleic acid source prior to cleavage.Consequently, a DNA molecule can be cleaved and cleaved exposed internalends can be re-ligated, for example at random, without loss of phaseinformation.

A bound nucleic acid molecule can be cleaved to expose internal endsthrough one of any number of enzymatic and non-enzymatic approaches. Forexample, a nucleic acid molecule can be digested using a restrictionenzyme, such as a restriction endonuclease that leaves a single strandedoverhang. MboI digest, for example, is suitable for this purpose,although other restriction endonucleases are contemplated. Lists ofrestriction endonucleases are available, for example, in most molecularbiology product catalogues. Other non-limiting techniques for nucleicacid cleavage include using a transposase, tagmentation enzyme complex,topoisomerase, nonspecific endonuclease, DNA repair enzyme, RNA-guidednuclease, fragmentase, or alternate enzyme. Transposase, for example,can be used in combination with unlinked left and right borders tocreate a sequence-independent break in a nucleic acid that is marked byattachment of transposase-delivered oligonucleotide sequence. Physicalmeans can also be used to generate cleavage, including mechanical means(e.g., sonication, shear), thermal means (e.g., temperature change), orelectromagnetic means (e.g., irradiation, such as UV irradiation).

Immobilization of nucleic acids at this stage can keep the cleavednucleic acid molecule fragments in close physical proximity, such thatphase information for the initial molecule is preserved. Exemplaryresulting chromatin aggregates from one nucleic acid binding moiety areshown schematically in FIG. 1. A benefit of the fixation, e.g. tochromatin aggregates, is that separate regions of a common nucleic acidmolecule can be held together independent of their phosphodiesterbackbone, such that their phase information is not lost upon cleavage ofthe phosphodiester backbone. This benefit is also conveyed throughalternate scaffolds to which a nucleic acid molecule is attached priorto cleavage.

Optionally, single stranded “sticky” end overhangs are modified toprevent reannealing and re-ligation. For example, sticky ends arepartially filled-in, such as by adding one nucleotide and a polymerase(FIG. 2). In this way, the entire single-stranded end cannot be filledin, but the end is modified to prevent re-ligation with a formerlycomplementary end. In the example of MboI digestion, which leaves a 5′GATC 5-prime overhang, only the Guanosine nucleotide triphosphate isadded. This results in only a “G” fill-in of the first complementarybase (“C”) and result in a 5′ GAT overhang. This step is renders thefree sticky ends incompatible for re-ligation to one another, butpreserves sticky ends for downstream applications. Alternately, bluntends are generated through completely filling in the overhangs,restriction digest with blunt-end generating enzymes, treatment with asingle-strand DNA exonuclease, or nonspecific cleavage. In some cases, atransposase is used to attach adapter ends having blunt or sticky endsto the exposed internal ends of the DNA molecule.

Optionally, a “punctuation oligonucleotide” is introduced (FIG. 3). Thispunctuation oligonucleotide marks cleavage/re-ligation sites. Somepunctuation oligonucleotides have single-stranded overhangs on both endsthat are compatible with the partially filled-in overhangs generated onthe exposed nucleic acid sample internal ends. An example of apunctuation oligonucleotide is shown below. In some cases, thedouble-stranded oligonucleotide having single-stranded overhangs ismodified, such as by 5′ phosphate removal at its 5′ ends, so that itcannot form concatemers during ligation. Alternately, blunt punctuationoligonucleotides are used, or cleavage sites are not marked using adistinct punctuation oligonucleotide. In some systems, such as when atransposase is used, punctuation is accomplished through addition oftranspososome border sequences, followed by ligation of border sequencesto one another or to a punctuation oligo. An exemplary punctuation oligois presented below. However, alternate punctuation oligos are consistentwith the disclosure herein, varying in sequence, length, overhangpresence or sequence, or modification such as 5′ de-phosphorylation.

5′ ATCACGCGC 3′    3′ TGCGCGCTA 5′In some cases, the double-stranded region of the punctuationoligonucleotide will vary. A relevant feature of the punctuationoligonucleotide is the sequence of its overhang, allowing ligation tothe nucleic acid sample but optionally modified precluding auto-ligationor concatemer formation. It is often preferred that the punctuationoligonucleotide comprise sequence that does not occur or is less likelyto occur in a target nucleic acid molecule, such that it is easilyidentified in a downstream sequence reaction. Punctuation oligos areoptionally barcoded, for example with a known barcode sequence or with arandomly generated unique identifier sequence. Unique identifiersequences can be designed to make it highly unlikely for multiplejunctions in a nucleic acid molecule or in a sample to be barcoded withthe same unique identifier.

Cleaved ends can be attached to one another directly or through an oligo(e.g., a punctuation oligo), for example using a ligase or similarenzyme. Ligation can proceed such that the free single-stranded ends ofan immobilized high-molecular weight nucleic acid molecule are ligateddirectly or to the punctuation oligonucleotide (FIG. 3). Because thepunctuation oligonucleotide, if utilized, can have two ligatable ends,this ligation can effectively chain regions of the high molecular weightnucleic acid molecule together. Alternative approaches resulting inaffixing a punctuating sequence or molecule between two exposed ends canalso be employed, as can approaches for directly connecting two exposedends without punctuation.

Nucleic acids can then be liberated from the nucleic acid bindingmoiety. In the case of in vitro chromatin aggregates, this can beaccomplished by reversing the cross-links, or digesting the proteincomponents, or both reversing the crosslinking and digesting proteincomponents. A suitable approach is treatment of complexes withproteinase K, though many alternatives are also contemplated. For otherbinding techniques, suitable methods can be employed, such as thesevering of linker molecules or the degradation of a substrate.

Nucleic acid molecules resulting from such techniques can have a varietyof relevant features. Sequence segments within a nucleic acid moleculecan be rearranged relative to their natural or starting positions andorientations, but with phase information preserved. Consequently,sequence segments on either side of a junction can be confidentlyassigned to a common phase of a common sample molecule. Thus, segmentsfar removed from one another on a molecule can be, by such techniques,brought together or in proximity such that portions or the entirety ofeach segment is sequenced in a single run of a single moleculesequencing device, allowing definitive phase assignment. Alternately, insome cases originally adjacent segments can become separated from one inthe resultant nucleic acid. In some cases, the nucleic acid moleculescan be re-ligated such that at least about 50%, 55%, 60%, 65%, 70%, 75%,80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.9%,99.99%, 99.999%, or 100% of re-ligations are between segments that werein phase on a common nucleic acid source prior to cleavage.

Another relevant feature of the resultant molecules is that, in somecases, most or all the original molecular sequence is preserved, thoughperhaps rearranged, in the final punctuated or rearranged molecule. Forexample, in some cases no more than 1%, 2%, 3%, 4%, 5%, 10%, 15%, or 20%of the original molecule is lost in producing the resultant molecule ormolecules. Consequently, in addition to being useful as a phasedeterminant, the resultant molecule retains a substantial proportion ofthe original molecule sequence, such that the resultant molecule isoptionally used to concurrently generate sequence information such ascontig information useful in de novo sequencing or as independentverification of previously generated contig information.

Another feature of libraries of some resultant molecules is thatcleavage junctions are not common to multiple members of a population ofresultant molecules. That is, that different copies of the same startingnucleic acid molecule can end up with different patterns of junction andrearrangement. Random cleavage junctions can be generated with anon-specific cleavage molecule, or through variation in restrictionendonuclease selection or digestion parameters.

A consequence of having molecule-specific cleavage sites is that in somecases punctuation oligonucleotides are optionally excluded from theprocess that results in the ‘punctuation molecule’ re-shuffling andre-ligation to no ill effect. By aligning segments of three or morereshuffled molecules, one observes that cleavage sites are readilyidentified by their absence in the majority of other members of alibrary. That is, when three or more reshuffled molecules are locallyaligned, a segment can be found to be common to all of the molecules,but the edges of the segment can vary among the molecules. By notingwhere segment local sequence similarity ends, one can map cleavagejunctions in an ‘unpunctuated’ rearranged nucleic acid molecule.

The resulting nucleic acid molecules (see, e.g., FIG. 4) can besequenced, for example on a long-read sequencer. The resulting sequencereads contain segments that alternate between nucleic acid sequence fromthe original input molecule and, if they are used, sequences of thepunctuation oligo. These reads can be processed by a computer to splitsequence data from each read using the punctuation oligonucleotidesequence, or are otherwise processed to identify junctions. The sequencesegments within each read can be segments from a single input highmolecular weight DNA molecule. The original nucleic acid molecule cancomprise a genome sequence or fraction thereof, such as a chromosome.The sets of segment reads can be discontinuous in the original nucleicacid molecule but reveal long-range, haplotype-phased data. These datacan be used for de novo genome assembly and phasing heterozygouspositions in the input genome. Sequence between junctions indicatescontiguous nucleic acid sequence in the source nucleic acid sample,while sequence across a junction is indicative of a nucleic acid segmentthat is in phase in the nucleic acid sample but that may be far removedin the arranged scaffold from the adjacent segment.

Junctions can be identified by a variety of approaches. If punctuationoligos are used, junctions can be identified at reads containing thepunctuation oligo sequence. Alternately, junctions can be identified bycomparison to a second sequence source (and, preferably, a thirdsequence source) for a nucleic acid molecule, such as a previouslygenerated contig sequence dataset or a second, independently generatedDNA chain molecule having independently derived junctions. As thesequence is aligned, for example, the quality or confidence of alignmentto a particular location can indicate where one segment ends and anotherbegins. If restriction enzymes are used to generate cleavages, sequencescontaining the restriction enzyme recognition site can be evaluated forpotentially containing a junction. Note that not every restrictionenzyme recognition site may contain a junction, as some restrictionenzyme recognition sites may not have been physically accessible by theenzyme while the nucleic acid was bound to the support, for example.Statistical information can also be employed in identifying junctions;for example, the length segments between junctions may be predicted tobe of a certain average value or to follow a certain distribution.

A benefit of the manipulations herein is that they can preservemolecular phase information while bringing nonadjacent regions of themolecule in proximity such that they are included in a single nucleicacid molecule at a distance suitable for sequencing in a single read,such as a long read. Thus, regions that are separated in the startingsample by greater than the distance of a single long read operation (forexample 10 kb, 15 kb, 20 kb, 30 kb, 50 kb, 100 kb or greater) arebrought into local proximity such that they are within the distancecovered by a single read of a long-range sequencing reaction. Thus,regions that are separated by more than the range of the sequencingtechnology for a single read in the original sample are read in a singlereaction in the phase-preserved, rearranged molecule.

Resultant rearranged molecules can be sequenced and their sequenceinformation mapped to independently or concurrently generated sequencereads or contig information, or to a known reference genome sequence(for example, the known sequence of the human genome). Segments adjacenton the resultant rearranged molecule reads are presumed to be in phase.Accordingly, when these segments are mapped to disparate contigs or longrange sequence reads, the reads are assigned to a common phase of acommon molecule in the sequence assembly.

Alternately, if multiple independently generated resultant rearrangedmolecules are sequenced concurrently, phased sample data is optionallygenerated from these molecules alone, such that segment sequencesseparated by junctions are inferred to be in phase, while sequences notseparated by junctions are inferred to represent stretches of nucleicacids contiguous in the sample itself and useful for, for example, denovo sequence determination as well as being useful for phasedetermination. However, additionally or as an alternative, multipleindependently generated resultant rearranged molecules sequencedconcurrently can still be compared to independently generated scaffoldor contig information

Methods and compositions presented herein can preserve long-range phaseinformation, particularly for molecule segments separated by greaterthan the length of a read in a sequencing technology (10 kb, 20 kb, 50kb, 100 kb, 500 kb or greater, for example), while providing suchnonadjacent segments in a rearranged or often ‘punctuated’ moleculewhere the segments are adjacent or close enough to be covered by asingle read.

In some instances, resultant rearranged molecules are combined withnative molecules for sequencing. The native molecules can be recognizedand utilized informatically by the lack of punctuation sequences, ifemployed. Native molecules are sequenced using short or long readtechnology, and their assembly is guided by the phase information andsegment sequence information generated through sequencing of therearranged molecule or library.

Nucleic Acid Extraction

Methods for the extraction and purification of nucleic acids suitablefor use with the disclosure herein are well known in the art. Forexample, nucleic acids are purified by organic extraction with phenol,phenol/chloroform/isoamyl alcohol, or similar formulations, includingTRIzol and TriReagent. Other non-limiting examples of extractiontechniques include: (1) organic extraction followed by ethanolprecipitation, e.g., using a phenol/chloroform organic reagent (Ausubelet al., 1993), with or without the use of an automated nucleic acidextractor, e.g., the Model 341 DNA Extractor available from AppliedBiosystems (Foster City, Calif.); (2) stationary phase adsorptionmethods (U.S. Pat. No. 5,234,809; Walsh et al., 1991); and (3)salt-induced nucleic acid precipitation methods (Miller et al., (1988),such precipitation methods being typically referred to as “salting-out”methods. Another example of nucleic acid isolation and/or purificationincludes the use of magnetic particles to which nucleic acidsspecifically or non-specifically bind, followed by isolation of thebeads using a magnet, and washing and eluting the nucleic acids from thebeads (see e.g. U.S. Pat. No. 5,705,628). In some embodiments, the aboveisolation methods may be preceded by an enzyme digestion step to helpeliminate unwanted protein from the sample, e.g., digestion withproteinase K, or other like proteases. See, e.g., U.S. Pat. No.7,001,724. If desired, RNase inhibitors may be added to the lysisbuffer. For certain cell or sample types, it may be desirable to add aprotein denaturation/digestion step to the protocol. Purificationmethods may be directed to isolate DNA, RNA, or both. When both DNA andRNA are isolated together during or subsequent to an extractionprocedure, further steps may be employed to purify one or bothseparately from the other. Sub-fractions of extracted nucleic acids canalso be generated, for example, purification by size, sequence, or otherphysical or chemical characteristic. In addition to an initial nucleicacid isolation step, purification of nucleic acids can be performedafter any step in the methods of the disclosure, such as to removeexcess or unwanted reagents, reactants, or products.

Nucleic acid template molecules can be obtained as described, forexample, in U.S. Patent Application Publication Number US2002/0190663A1, published Oct. 9, 2003. Generally, nucleic acids are extracted froma biological sample by a variety of techniques such as those describedby Maniatis, et al., Molecular Cloning: A Laboratory Manual, Cold SpringHarbor, N.Y., pp. 280-281 (1982, which is herein incorporated byreference in its entirety). In some cases, the nucleic acids can befirst extract from the biological samples and then cross-linked invitro. In some cases, native association proteins (e.g. histones) can befurther removed from the nucleic acids. In some embodiments, thedisclosure is easily applied to any high molecular weight doublestranded DNA including, for example, DNA isolated from tissues, cellculture, bodily fluids, animal tissue, plant, bacteria, fungi, orviruses.

In some embodiments, nucleic acid template molecules (e.g., DNA or RNA)are isolated from a biological sample containing a variety of othercomponents, such as proteins, lipids, and non-template nucleic acids.Nucleic acid template molecules can be obtained from any cellularmaterial, obtained from an animal, plant, bacterium, fungus, or anyother cellular organism or virus, or may be artificially synthesized.Biological samples for use in the present disclosure include viralparticles or preparations. Nucleic acid template molecules can beobtained directly from an organism or from a biological sample obtainedfrom an organism, e.g., from blood, urine, cerebrospinal fluid, seminalfluid, saliva, sputum, stool and tissue. Any tissue or body fluidspecimen may be a source for nucleic acids of the present disclosure.Nucleic acid template molecules can also be isolated from culturedcells, such as a primary cell culture or a cell line. The cells ortissues from which template nucleic acids are obtained can be infectedwith a virus or other intracellular pathogen. A sample can also be totalRNA extracted from a biological specimen, a cDNA library, viral, orgenomic DNA. A sample may also comprise isolated DNA from a non-cellularorigin, e.g. amplified/isolated DNA from the freezer.

Nucleic acid molecules, including high molecular weight DNA, can bebound or immobilized on a nucleic acid binding moiety. For example, DNAassembled into in vitro chromatin aggregates and fixed with formaldehydetreatment are consistent with methods herein. Nucleic acid binding orimmobilizing approaches include, but are not limited to, in vitro orreconstituted chromatin assembly, native chromatin, DNA-binding proteinaggregates, nanoparticles, DNA-binding beads or beads coated using aDNA-binding substance, polymers, synthetic DNA-binding molecules orother solid or substantially solid affinity molecules. In some cases,the beads are solid phase reversible immobilization (SPRI) beads (e.g.,beads with negatively charged carboxyl groups such as Beckman-CoulterAgencourt AMPure XP beads).

Nucleic acids, such as those bound to a nucleic acid binding moiety suchas those described herein, can be held such that a nucleic acid moleculehaving a first segment and a second segment separated on the nucleicacid molecule by a distance greater than a read distance on a sequencingdevice (10 kb, 50 kb, 100 kb or greater, for example) are bound togetherindependent of their common phosphodiester bonds. Upon cleavage of sucha bound nucleic acid molecule, exposed ends of the first segment and thesecond segment may ligate to one another. In some cases, the nucleicacid molecules are bound at a concentration such that there is little orno overlap between bound nucleic acid molecules on a solid surface, suchthat exposed internal ends of cleaved molecules are likely to re-ligateor become reattached only to exposed ends from other segments that werein phase on a common nucleic acid source prior to cleavage.Consequently, a DNA molecule can be cleaved and cleaved exposed internalends can be re-ligated, for example at random, without loss of phaseinformation. In some cases, the nucleic acid molecules can be re-ligatedsuch that at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.9%, 99.99%, 99.999%, or100% of re-ligations are between segments that were in phase on a commonnucleic acid source prior to cleavage.

In some cases, the surface density of bound nucleic acids on a surfaceis controlled through the amount of surface area made available forbinding. For example, selecting the size of a bead used for bindingnucleic acids can affect or control the distance between nucleic acids,or the average surface density of bound nucleic acids. A larger beadsurface can result in a greater distance between bound nucleic acids.This can result in a reduced rate of intermolecular ligation eventsbetween nucleic acids or nucleic acid complexes. The beads used can beabout 100 nanometers (nm), 200 nm, 300 nm, 400 nm, 500 nm, 600 nm, 700nm, 800 nm, 900 nm, 1 micrometer (μm), 1.1 μm, 1.2 μm, 1.3 μm, 1.4 μm,1.5 μm, 1.6 μm, 1.7 μm, 1.8 μm, 1.9 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7μm, 8 μm, 9 μm, 10 μm, 11 μm, 12 μm, 13 μm, 14 μm, 15 μm, 16 μm, 17 μm,18 μm, 19 μm, 20 μm, 21 μm, 22 μm, 23 μm, 24 μm, 25 μm, 26 μm, 27 μm, 28μm, 29 μm, 30 μm, 31 μm, 32 μm, 33 μm, 34 μm, 35 μm, 36 μm, 37 μm, 38μm, 39 μm, 40 μm, 41 μm, 42 μm, 43 μm, 44 μm, 45 μm, 46 μm, 47 μm, 48μm, 49 μm, 50 μm, 55 μm, 60 μm, 65 μm, 70 μm, 75 μm, 80 μm, 85 μm, 90μm, 95 μm, 100 μm, 200 μm, 300 μm, 400 μm, 500 μm, 600 μm, 700 μm, 800μm, 900 μm, or 1 millimeter (mm) in diameter. The beads used can be atleast about 100 nanometers (nm), 200 nm, 300 nm, 400 nm, 500 nm, 600 nm,700 nm, 800 nm, 900 nm, 1 micrometer (μm), 1.1 μm, 1.2 μm, 1.3 μm, 1.4μm, 1.5 μm, 1.6 μm, 1.7 μm, 1.8 μm, 1.9 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6μm, 7 μm, 8 μm, 9 μm, 10 μm, 11 μm, 12 μm, 13 μm, 14 μm, 15 μm, 16 μm,17 μm, 18 μm, 19 μm, 20 μm, 21 μm, 22 μm, 23 μm, 24 μm, 25 μm, 26 μm, 27μm, 28 μm, 29 μm, 30 μm, 31 μm, 32 μm, 33 μm, 34 μm, 35 μm, 36 μm, 37μm, 38 μm, 39 μm, 40 μm, 41 μm, 42 μm, 43 μm, 44 μm, 45 μm, 46 μm, 47μm, 48 μm, 49 μm, 50 μm, 55 μm, 60 μm, 65 μm, 70 μm, 75 μm, 80 μm, 85μm, 90 μm, 95 μm, 100 μm, 200 μm, 300 μm, 400 μm, 500 μm, 600 μm, 700μm, 800 μm, 900 μm, or 1 millimeter (mm) in diameter. The beads used canbe at most about 100 nanometers (nm), 200 nm, 300 nm, 400 nm, 500 nm,600 nm, 700 nm, 800 nm, 900 nm, 1 micrometer (μm), 1.1 μm, 1.2 μm, 1.3μm, 1.4 μm, 1.5 μm, 1.6 μm, 1.7 μm, 1.8 μm, 1.9 μm, 2 μm, 3 μm, 4 μm, 5μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 11 μm, 12 μm, 13 μm, 14 μm, 15 μm, 16μm, 17 μm, 18 μm, 19 μm, 20 μm, 21 μm, 22 μm, 23 μm, 24 μm, 25 μm, 26μm, 27 μm, 28 μm, 29 μm, 30 μm, 31 μm, 32 μm, 33 μm, 34 μm, 35 μm, 36μm, 37 μm, 38 μm, 39 μm, 40 μm, 41 μm, 42 μm, 43 μm, 44 μm, 45 μm, 46μm, 47 μm, 48 μm, 49 μm, 50 μm, 55 μm, 60 μm, 65 μm, 70 μm, 75 μm, 80μm, 85 μm, 90 μm, 95 μm, 100 μm, 200 μm, 300 μm, 400 μm, 500 μm, 600 μm,700 μm, 800 μm, 900 μm, or 1 millimeter (mm) in diameter.

Nucleic Acid Binding Moiety Complex Formation

A nucleic acid can be bound to a nucleic acid binding moiety to preservephase information after cleavage of the nucleic acid molecule. Manynucleic acid binding moieties form scaffolds consistent with thedisclosure herein. Some suitable with the disclosure herein bind anucleic acid at multiple points such that phase information is not lostupon cleavage and re-ligation of the nucleic acid molecule.

In some cases, the nucleic acid binding moiety is or comprises acategory of protein, such as histones that form chromatin. The chromatincan be reconstituted chromatin or native chromatin. In some cases, thenucleic acid binding moiety is distributed on solid support such as amicroarray, a slide, a chip, a microwell, a column, a tube, a particleor a bead. In some examples, the solid support is coated withstreptavidin and/or avidin. In other examples, the solid support iscoated with an antibody. Further, the solid support can additionally oralternatively comprise a glass, metal, ceramic or polymeric material. Insome embodiments, the solid support is a nucleic acid microarray (e.g. aDNA microarray). In other embodiments, the solid support can be aparamagnetic bead.

In some cases, the DNA sample is cross-linked to a plurality ofassociation molecules. In various cases, the association moleculescomprise amino acids. In many cases, the association molecules comprisepeptides or proteins. In further cases, the association moleculescomprise histones. In other cases, the association molecules comprisenanoparticles. In some cases, the nanoparticle is a platinum-basednanoparticle. In other cases, the nanoparticle is a DNA intercalator, orany derivatives thereof. In further cases, the nanoparticle is abisintercalator, or any derivatives thereof. In certain cases, theassociation molecules are from a different source than the first DNAmolecule. The cross-linking can be conducted as part of a protocol asdisclosed herein, or can have been conducted previously. For example,previously fixed samples (e.g., formalin-fixed paraffin-embedded (FFPE))samples can be processed and analyzed with techniques of the presentdisclosure.

An example of a nucleic acid binding moiety that forms a structure isreconstituted chromatin. Reconstituted chromatin is differentiated fromchromatin formed within a cell/organism over various features. First,reconstituted chromatin is generated in some cases from isolated nakedDNA. For many samples, the collection of naked DNA samples is achievedby using any one of a variety of noninvasive to invasive methods, suchas by collecting bodily fluids, swabbing buccal or rectal areas, takingepithelial samples, etc. These approaches are generally easier, faster,and less expensive than isolation of native chromatin.

Second, reconstituting chromatin substantially reduces the formation ofinter-chromosomal and other long-range interactions that generateartifacts for genome assembly and haplotype phasing. In some cases, asample has less than about 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20,19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0.5,0.4, 0.3, 0.2, 0.1, 0.01, 0.001% or less inter-chromosomal orintermolecular crosslinking according to the methods and compositions ofthe disclosure. In some examples, the sample has less than about 30%inter-chromosomal or intermolecular crosslinking. In some examples, thesample has less than about 25% inter-chromosomal or intermolecularcrosslinking. In some examples, the sample has less than about 20%inter-chromosomal or intermolecular crosslinking. In some examples, thesample has less than about 15% inter-chromosomal or intermolecularcrosslinking. In some examples, the sample has less than about 10%inter-chromosomal or intermolecular crosslinking. In some examples, thesample has less than about 5% inter-chromosomal or intermolecularcrosslinking. In some examples, the sample may have less than about 3%inter-chromosomal or intermolecular crosslinking. In further examples,may have less than about 1% inter-chromosomal or intermolecularcrosslinking. As inter-chromosomal interactions represent interactionsbetween molecular sections that are not in phase, their reduction orelimination is beneficial to some goals of the present disclosure, thatis, the efficient, rapid assembly of phased nucleic acid information.

Third, the frequency of sites that are capable of crosslinking and thusthe frequency of intramolecular crosslinks within the polynucleotide isadjustable. For example, the ratio of DNA to histones can be varied,such that the nucleosome density can be adjusted to a desired value. Insome cases, the nucleosome density is reduced below the physiologicallevel. Accordingly, the distribution of crosslinks can be altered tofavor longer-range interactions. In some embodiments, sub-samples withvarying cross-linking density may be prepared to cover both short- andlong-range associations.

For example, the crosslinking conditions can be adjusted such that atleast about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%,about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about20%, about 25%, about 30%, about 40%, about 45%, about 50%, about 60%,about 70%, about 80%, about 90%, about 95%, or about 100% of thecrosslinks so as to join DNA segments that are at least about 50 kb,about 60 kb, about 70 kb, about 80 kb, about 90 kb, about 100 kb, about110 kb, about 120 kb, about 130 kb, about 140 kb, about 150 kb, about160 kb, about 180 kb, about 200 kb, about 250 kb, about 300 kb, about350 kb, about 400 kb, about 450 kb, or about 500 kb apart on a sampleDNA molecule.

An important benefit of a nucleic acid binding moiety scaffold such asreconstituted chromatin is that it preserves physical linkageinformation of its constituent nucleic acids independent of theirphosphodiester bonds. Accordingly, nucleic acids held together byreconstituted chromatin, optionally crosslinked to maintain stability,will maintain their proximity even if their phosphodiester bonds arebroken, as may occur in internal labeling. Because of the reconstitutedchromatin, the fragments will remain in proximity even though cleaved,thereby preserving phase or physical linkage information during aninternal labeling process. Thus, when the exposed ends are re-ligated,they will ligate to segments derived from a common phase of a commonmolecule.

Reconstituted Chromatin Assembly

The assembly of nucleic acids onto a nucleic acid binding moiety for thepreservation of phase information during cleavage and rearrangement ofthe nucleic acid molecule is accomplished in some cases through theassembly of reconstituted chromatin onto a nucleic acid sample.Reconstituted chromatin as used herein is used broadly, ranging fromreassembly of native chromatin constituents onto a nucleic acid, tobinding of a nucleic acid to non-biological particles.

Referring to reconstituted chromatin in a traditional sense, assembly ofcore histones and DNA into nucleosomes is mediated by chaperone proteinsand associated assembly factors. Nearly all these factors are corehistone-binding proteins. Some of the histone chaperones, such asnucleosome assembly protein-1 (NAP-1), exhibit a preference for bindingto histones H3 and H4. It has also been observed that newly synthesizedhistones are acetylated and then subsequently deacetylated afterassembly into chromatin. The factors that mediate histone acetylation ordeacetylation therefore play an important role in the chromatin assemblyprocess.

In general, two in vitro methods have been developed for reconstitutingor assembling chromatin, although variations on these methods arecontemplated. One set of methods involves ATP-independent assembly,while a second set of methods is ATP-dependent.

The ATP-independent methods for reconstituting chromatin involve the DNAand core histones plus either a protein like NAP-1 or salt to act as ahistone chaperone. This method results in a random arrangement ofhistones on the DNA that does not accurately mimic the native corenucleosome particle in the cell. These particles are often referred toas mononucleosomes because they are not regularly ordered, extendednucleosome arrays and the DNA sequence used is usually not longer than250 bp (Kundu, T. K. et al., Mol. Cell 6: 551-561, 2000). To generate anextended array of ordered nucleosomes on a greater length of DNAsequence, the chromatin must be assembled through an ATP-dependentprocess.

The ATP-dependent assembly of periodic nucleosome arrays, which aresimilar to those seen in native chromatin, requires the DNA sequence,core histone particles, a chaperone protein, and ATP-utilizing chromatinassembly factors. ACF (ATP-utilizing chromatin assembly and remodelingfactor) or RSF (remodeling and spacing factor) are two widely researchedassembly factors that are used to generate extended ordered arrays ofnucleosomes into chromatin in vitro (Fyodorov, D. V., and Kadonaga, J.T. Method Enzymol. 371: 499-515, 2003; Kundu, T. K. et al. Mol. Cell 6:551-561, 2000).

Alternate assembly approaches, for example approaches that do not relyupon histones to constitute reconstituted chromatin, are alsocontemplated. Any DNA binding moiety can be added to a nucleic acid toform some types of reconstituted chromatin broadly defined.

In some embodiments, non-natural chromatin analogs are contemplated.Nanoparticles, such as nanoparticles having a positively coated outersurface to facilitate nucleic acid binding, or a surface activatable forcross-linking to nucleic acids, or both a positively coated outersurface to facilitate nucleic acid binding and a surface activatable forcross-linking to nucleic acids, are contemplated herein. In someembodiments, nanoparticles comprise silicon.

In some cases, the methods disclosed herein are used with DNA associatedwith nanoparticles. In some instances, the nanoparticles are positivelycharged. For example, the nanoparticles are coated with amine groups,and/or amine-containing molecules. The DNA and the nanoparticlesaggregate and condense, similar to native or reconstituted chromatin.Further, the nanoparticle-bound DNA is induced to aggregate in a fashionthat mimics the ordered arrays of biological nucleosomes (i.e.chromatin). The nanoparticle-based method can be less expensive, fasterto assemble, provides a better recovery rate than using reconstitutedchromatin, and/or allows for reduced DNA input requirements.

A number of factors can be varied to influence the extent and form ofcondensation including the concentration of nanoparticles in solution,the ratio of nanoparticles to DNA, and the size of nanoparticles used.In some cases, the nanoparticles are added to the DNA at a concentrationgreater than about 1 ng/mL, 2 ng/mL, 3 ng/mL, 4 ng/mL, 5 ng/mL, 6 ng/mL,7 ng/mL, 8 ng/mL, 9 ng/mL, 10 ng/mL, 15 ng/mL, 20 ng/mL, 25 ng/mL, 30ng/mL, 40 ng/mL, 50 ng/mL, 60 ng/mL, 70 ng/mL, 80 ng/mL, 90 ng/mL, 100ng/mL, 120 ng/mL, 140 ng/mL, 160 ng/mL, 180 ng/mL, 200 ng/mL, 250 ng/mL,300 ng/mL, 400 ng/mL, 500 ng/mL, 600 ng/mL, 700 ng/mL, 800 ng/mL, 900ng/mL, 1 μg/mL, 2 μg/mL, 3 μg/mL, 4 μg/mL, 5 μg/mL, 6 μg/mL, 7 μg/mL, 8μg/mL, 9 μg/mL, 10 μg/mL, 15 μg/mL, 20 μg/mL, 25 μg/mL, 30 μg/mL, 40μg/mL, 50 μg/mL, 60 μg/mL, 70 μg/mL, 80 μg/mL, 90 μg/mL, 100 μg/mL, 120μg/mL, 140 μg/mL, 160 μg/mL, 180 μg/mL, 200 μg/mL, 250 μg/mL, 300 μg/mL,400 μg/mL, 500 μg/mL, 600 μg/mL, 700 μg/mL, 800 μg/mL, 900 μg/mL, 1mg/mL, 2 mg/mL, 3 mg/mL, 4 mg/mL, 5 mg/mL, 6 mg/mL, 7 mg/mL, 8 mg/mL, 9mg/mL, 10 mg/mL, 15 mg/mL, 20 mg/mL, 25 mg/mL, 30 mg/mL, 40 mg/mL, 50mg/mL, 60 mg/mL, 70 mg/mL, 80 mg/mL, 90 mg/mL, or 100 mg/mL. In somecases, the nanoparticles are added to the DNA at a concentration lessthan about 1 ng/mL, 2 ng/mL, 3 ng/mL, 4 ng/mL, 5 ng/mL, 6 ng/mL, 7ng/mL, 8 ng/mL, 9 ng/mL, 10 ng/mL, 15 ng/mL, 20 ng/mL, 25 ng/mL, 30ng/mL, 40 ng/mL, 50 ng/mL, 60 ng/mL, 70 ng/mL, 80 ng/mL, 90 ng/mL, 100ng/mL, 120 ng/mL, 140 ng/mL, 160 ng/mL, 180 ng/mL, 200 ng/mL, 250 ng/mL,300 ng/mL, 400 ng/mL, 500 ng/mL, 600 ng/mL, 700 ng/mL, 800 ng/mL, 900ng/mL, 1 μg/mL, 2 μg/mL, 3 μg/mL, 4 μg/mL, 5 μg/mL, 6 μg/mL, 7 μg/mL, 8μg/mL, 9 μg/mL, 10 μg/mL, 15 μg/mL, 20 μg/mL, 25 μg/mL, 30 μg/mL, 40μg/mL, 50 μg/mL, 60 μg/mL, 70 μg/mL, 80 μg/mL, 90 μg/mL, 100 μg/mL, 120μg/mL, 140 μg/mL, 160 μg/mL, 180 μg/mL, 200 μg/mL, 250 μg/mL, 300 μg/mL,400 μg/mL, 500 μg/mL, 600 μg/mL, 700 μg/mL, 800 μg/mL, 900 μg/mL, 1mg/mL, 2 mg/mL, 3 mg/mL, 4 mg/mL, 5 mg/mL, 6 mg/mL, 7 mg/mL, 8 mg/mL, 9mg/mL, 10 mg/mL, 15 mg/mL, 20 mg/mL, 25 mg/mL, 30 mg/mL, 40 mg/mL, 50mg/mL, 60 mg/mL, 70 mg/mL, 80 mg/mL, 90 mg/mL, or 100 mg/mL. In somecases, the nanoparticles are added to the DNA at a weight-to-weight(w/w) ratio greater than about 1:10000, 1:5000, 1:2000, 1:1000, 1:500,1:200, 1:100, 1:50, 1:20, 1:10, 1:5, 1:2, 1:1, 2:1, 5:1, 10:1, 20:1,50:1, 100:1, 200:1, 500:1, 1000:1, 2000:1, 5000:1, or 10000:1. In somecases, the nanoparticles are added to the DNA at a weight-to-weight(w/w) ratio less than about 1:10000, 1:5000, 1:2000, 1:1000, 1:500,1:200, 1:100, 1:50, 1:20, 1:10, 1:5, 1:2, 1:1, 2:1, 5:1, 10:1, 20:1,50:1, 100:1, 200:1, 500:1, 1000:1, 2000:1, 5000:1, or 10000:1. In somecases, the nanoparticles have a diameter greater than about 1 nm 1 nm, 2nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10 nm, 15 nm, 20 nm, 25nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm, 80 nm, 90 nm, 100 nm, 120 nm, 140nm, 160 nm, 180 nm, 200 nm, 250 nm, 300 nm, 400 nm, 500 nm, 600 nm, 700nm, 800 nm, 900 nm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9μm, 10 μm, 15 μm, 20 μm, 25 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70 μm, 80μm, 90 μm, or 100 μm. In some cases, the nanoparticles have a diameterless than about 1 nm 1 nm, 2 nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9nm, 10 nm, 15 nm, 20 nm, 25 nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm, 80nm, 90 nm, 100 nm, 120 nm, 140 nm, 160 nm, 180 nm, 200 nm, 250 nm, 300nm, 400 nm, 500 nm, 600 nm, 700 nm, 800 nm, 900 nm, 1 μm, 2 μm, 3 μm, 4μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 15 μm, 20 μm, 25 μm, 30 μm, 40μm, 50 μm, 60 μm, 70 μm, 80 μm, 90 μm, or 100 μm.

Furthermore, the nanoparticles may be immobilized on solid substrates(e.g. beads, slides, or tube walls) by applying magnetic fields (in thecase of paramagnetic nanoparticles) or by covalent attachment (e.g. bycross-linking to poly-lysine coated substrate). Immobilization of thenanoparticles may improve the ligation efficiency thereby increasing thenumber of desired products (signal) relative to undesired (noise).

Reconstituted chromatin is optionally contacted to a crosslinking agentsuch as formaldehyde to further stabilize the DNA-chromatin complex.

Nucleic Acid Cleavage

Bound nucleic acids can be treated to expose internal double-strandends. Cleavage can be conducted with restriction enzymes, such asrestriction endonucleases. Alternative cleavage approaches are alsoconsistent with the disclosure herein. For example, a transposase isoptionally used in combination with unlinked left and right borderoligonucleic acid molecules so as to create a sequence-independent breakin a nucleic acid that is marked by the attachment of thetransposase-delivered oligonucleic acid molecules. The oligonucleic acidmolecules are synthesized in some cases to comprisepunctuation-compatible overhangs, or to be compatible with one another,such that the oligonucleic acid molecules are ligated to one another andserve as the punctuation molecules. A benefit of this type ofalternative approach is that cleavage is sequence independent, and thusmore likely to vary from one copy of a nucleic acid to another, even ifthe sequence of two nucleic acid molecules is locally identical.

In some cases, the exposed nucleic acid ends are desirably sticky ends,for example as results from contacting to a restriction endonuclease. Insome cases, a restriction endonuclease is used to cleave a predictableoverhang, followed by ligation with a nucleic acid end (such as apunctuation oligonucleotide) comprising an overhang complementary to thepredictable overhang on a DNA fragment. In some embodiments, the 5′and/or 3′ end of a restriction endonuclease-generated overhang ispartially filled in. In some cases, the overhang is filled in with asingle nucleotide.

In some instances, DNA fragments having an overhang can be joined to oneor more nucleic acids, such as punctuation oligonucleotides,oligonucleotides, adapter oligonucleotides, or polynucleotides, having acomplementary overhang, such as in a ligation reaction. For example, asingle adenine is added to the 3′ ends of end repaired DNA fragmentsusing a template independent polymerase, followed by ligation to one ormore punctuation oligonucleotides each having a thymine at a 3′ end. Insome embodiments, nucleic acids, such as oligonucleotides orpolynucleotides are joined to blunt end double-stranded DNA moleculeswhich have been modified by extension of the 3′ end with one or morenucleotides followed by 5′ phosphorylation. In some cases, extension ofthe 3′ end is performed with a polymerase such as, Klenow polymerase orany of the suitable polymerases provided herein, or by use of a terminaldeoxynucleotide transferase, in the presence of one or more dNTPs in asuitable buffer that contains magnesium. In some embodiments, targetpolynucleotides having blunt ends are joined to one or more adapterscomprising a blunt end. Phosphorylation of 5′ ends of DNA fragmentmolecules may be performed for example with T4 polynucleotide kinase ina suitable buffer containing ATP and magnesium. The fragmented DNAmolecules may optionally be treated to dephosphorylate 5′ ends or 3′ends, for example, by using enzymes known in the art, such asphosphatases.

Punctuation Oligonucleotides

In some cases, punctuation oligonucleotides can be utilized inconnecting exposed cleaved ends. A punctuation oligonucleotide includesany oligonucleotide that can be joined to a target polynucleotide, so asto bridge two cleaved internal ends of a sample molecule undergoingphase-preserving rearrangement. Punctuation oligonucleotides cancomprise DNA, RNA, nucleotide analogues, non-canonical nucleotides,labeled nucleotides, modified nucleotides, or combinations thereof. Inmany examples, double-stranded punctuation oligonucleotides comprise twoseparate oligonucleotides hybridized to one another (also referred to asan “oligonucleotide duplex”), and hybridization may leave one or moreblunt ends, one or more 3′ overhangs, one or more 5′ overhangs, one ormore bulges resulting from mismatched and/or unpaired nucleotides, orany combination of these. In some instances, different punctuationoligonucleotides are joined to target polynucleotides in sequentialreactions or simultaneously. For example, the first and secondpunctuation oligonucleotides can be added to the same reaction.Alternately, punctuation oligo populations are uniform in some cases.

Punctuation oligonucleotides can be manipulated prior to combining withtarget polynucleotides. For example, terminal phosphates can be removed.Such a modification precludes location of punctuation oligos to oneanother rather than to cleaved internal ends of a sample molecule.

Punctuation oligonucleotides contain one or more of a variety ofsequence elements, including but not limited to, one or moreamplification primer annealing sequences or complements thereof, one ormore sequencing primer annealing sequences or complements thereof, oneor more barcode sequences, one or more common sequences shared amongmultiple different punctuation oligonucleotides or subsets of differentpunctuation oligonucleotides, one or more restriction enzyme recognitionsites, one or more overhangs complementary to one or more targetpolynucleotide overhangs, one or more probe binding sites, one or morerandom or near-random sequences, and combinations thereof. In someexamples, two or more sequence elements are non-adjacent to one another(e.g. separated by one or more nucleotides), adjacent to one another,partially overlapping, or completely overlapping. For example, anamplification primer annealing sequence also serves as a sequencingprimer annealing sequence. In certain instances, sequence elements arelocated at or near the 3′ end, at or near the 5′ end, or in the interiorof the punctuation oligonucleotide.

In alternate embodiments, the punctuation oligo comprises a minimalcomplement of bases to maintain integrity of the double-strandedmolecule, so as to minimize the amount of sequence information itoccupies in a sequencing reaction, or the punctuation oligo comprises anoptimal number of bases for ligation, or the punctuation oligo length isarbitrarily determined.

In some embodiments, a punctuation oligonucleotide comprises a 5′overhang, a 3′ overhang, or both that is complementary to one or moretarget polynucleotides. In certain instances, complementary overhangsare one or more nucleotides in length, including but not limited to 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more nucleotides inlength. For example, the complementary overhang is about 1, 2, 3, 4, 5or 6 nucleotides in length. In some embodiments, a punctuationoligonucleotide overhang is complementary to a target polynucleotideoverhang produced by restriction endonuclease digestion or other DNAcleavage method.

Punctuation oligonucleotides can have any suitable length, at leastsufficient to accommodate the one or more sequence elements of whichthey are comprised. In some embodiments, punctuation oligonucleotidesare about, less than about, or more than about 4, 5, 6, 7, 8, 9, 10, 15,20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 200, ormore nucleotides in length. In some examples, the punctuationoligonucleotide is 5 to 15 nucleotides in length. In further examples,the punctuation oligonucleotide is about 20 to about 40 nucleotides inlength.

Preferably, punctuation oligonucleotides are modified, for example by 5′phosphate excision (via calf alkaline phosphatase treatment, or de novoby synthesis in the absence of such moieties), so that they do notligate with one another to form multimers. 3′ OH (hydroxyl) moieties areable to ligate to 5′ phosphates on the cleaved nucleic acids, therebysupporting ligation to a first or a second nucleic acid segment.

Adapter Oligonucleotides

An adapter includes any oligonucleotide having a sequence that can bejoined to a target polynucleotide. In various examples, adapteroligonucleotides comprise DNA, RNA, nucleotide analogues, non-canonicalnucleotides, labeled nucleotides, modified nucleotides, or combinationsthereof. In some instances, adapter oligonucleotides aresingle-stranded, double-stranded, or partial duplex. In general, apartial-duplex adapter oligonucleotide comprises one or moresingle-stranded regions and one or more double-stranded regions.Double-stranded adapter oligonucleotides can comprise two separateoligonucleotides hybridized to one another (also referred to as an“oligonucleotide duplex”), and hybridization may leave one or more bluntends, one or more 3′ overhangs, one or more 5′ overhangs, one or morebulges resulting from mismatched and/or unpaired nucleotides, or anycombination of these. In some embodiments, a single-stranded adapteroligonucleotide comprises two or more sequences that can hybridize withone another. When two such hybridizable sequences are contained in asingle-stranded adapter, hybridization yields a hairpin structure(hairpin adapter). When two hybridized regions of an adapteroligonucleotides are separated from one another by a non-hybridizedregion, a “bubble” structure results. Adapter oligonucleotidescomprising a bubble structure consist of a single adapteroligonucleotide comprising internal hybridizations, or comprise two ormore adapter oligonucleotides hybridized to one another. Internalsequence hybridization, such as between two hybridizable sequences inadapter oligonucleotides, produce, in some instances, a double-strandedstructure in a single-stranded adapter oligonucleotide. In someexamples, adapter oligonucleotides of different kinds are used incombination, such as a hairpin adapter and a double-stranded adapter, oradapters of different sequences. In certain cases, hybridizablesequences in a hairpin adapter include one or both ends of theoligonucleotide. When neither of the ends are included in thehybridizable sequences, both ends are “free” or “overhanging.” When onlyone end is hybridizable to another sequence in the adapter, the otherend forms an overhang, such as a 3′ overhang or a 5′ overhang. When boththe 5′-terminal nucleotide and the 3′-terminal nucleotide are includedin the hybridizable sequences, such that the 5′-terminal nucleotide andthe 3′-terminal nucleotide are complementary and hybridize with oneanother, the end is referred to as “blunt.” In some cases, differentadapter oligonucleotides are joined to target polynucleotides insequential reactions or simultaneously. For example, the first andsecond adapter oligonucleotides is added to the same reaction. In someexamples, adapter oligonucleotides are manipulated prior to combiningwith target polynucleotides. For example, terminal phosphates can beadded or removed.

Adapter oligonucleotides contain one or more of a variety of sequenceelements, including but not limited to, one or more amplification primerannealing sequences or complements thereof, one or more sequencingprimer annealing sequences or complements thereof, one or more barcodesequences, one or more common sequences shared among multiple differentadapters or subsets of different adapters, one or more restrictionenzyme recognition sites, one or more overhangs complementary to one ormore target polynucleotide overhangs, one or more probe binding sites(e.g. for attachment to a sequencing platform, such as a flow cell formassive parallel sequencing, such as developed by Illumina, Inc.), oneor more random or near-random sequences (e.g. one or more nucleotidesselected at random from a set of two or more different nucleotides atone or more positions, with each of the different nucleotides selectedat one or more positions represented in a pool of adapters comprisingthe random sequence), and combinations thereof. In many examples, two ormore sequence elements can be non-adjacent to one another (e.g.separated by one or more nucleotides), adjacent to one another,partially overlapping, or completely overlapping. For example, anamplification primer annealing sequence also serves as a sequencingprimer annealing sequence. Sequence elements are located at or near the3′ end, at or near the 5′ end, or in the interior of the adapteroligonucleotide. When an adapter oligonucleotides can form secondarystructure, such as a hairpin, sequence elements can be located partiallyor completely outside the secondary structure, partially or completelyinside the secondary structure, or in between sequences participating inthe secondary structure. For example, when an adapter oligonucleotidescomprises a hairpin structure, sequence elements can be locatedpartially or completely inside or outside the hybridizable sequences(the “stem”), including in the sequence between the hybridizablesequences (the “loop”). In some embodiments, the first adapteroligonucleotides in a plurality of first adapter oligonucleotides havingdifferent barcode sequences comprise a sequence element common among allfirst adapter oligonucleotides in the plurality. In some embodiments,all second adapter oligonucleotides comprise a sequence element commonto all second adapter oligonucleotides that is different from the commonsequence element shared by the first adapter oligonucleotides. Adifference in sequence elements can be any such that at least a portionof different adapters do not completely align, for example, due tochanges in sequence length, deletion or insertion of one or morenucleotides, or a change in the nucleotide composition at one or morenucleotide positions (such as a base change or base modification). Insome embodiments, an adapter oligonucleotides comprises a 5′ overhang, a3′ overhang, or both that is complementary to one or more targetpolynucleotides. Complementary overhangs can be one or more nucleotidesin length, including but not limited to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, or more nucleotides in length. For example, thecomplementary overhang can be about 1, 2, 3, 4, 5 or 6 nucleotides inlength. Complementary overhangs may comprise a fixed sequence.Complementary overhangs may additionally or alternatively comprise arandom sequence of one or more nucleotides, such that one or morenucleotides are selected at random from a set of two or more differentnucleotides at one or more positions, with each of the differentnucleotides selected at one or more positions represented in a pool ofadapter oligonucleotides with complementary overhangs comprising therandom sequence. In some embodiments, an adapter oligonucleotidesoverhang is complementary to a target polynucleotide overhang producedby restriction endonuclease digestion. In some embodiments, an adapteroligonucleotide overhang consists of an adenine or a thymine.

Adapter oligonucleotides can have any suitable length, at leastsufficient to accommodate the one or more sequence elements of whichthey are comprised. In some embodiments, adapter oligonucleotides areabout, less than about, or more than about 4, 5, 6, 7, 8, 9, 10, 15, 20,25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 200, or morenucleotides in length. In some examples, the adapter oligonucleotidesare 5 to 15 nucleotides in length. In further examples, the adapteroligonucleotides are about 20 to about 40 nucleotides in length.

Preferably, adapter oligonucleotides are modified, for example by 5′phosphate excision (via calf alkaline phosphatase treatment, or de novoby synthesis in the absence of such moieties), so that they do notligate with one another to form multimers. 3′ OH (hydroxyl) moieties areable to ligate to 5′ phosphates on the cleaved nucleic acids, therebysupporting ligation to a first or a second nucleic acid segment.

Determining Phase Information of a Nucleic Acid Sample

To determine phase information of a nucleic acid sample, a nucleic acidis first acquired, for example by extraction methods discussed herein.In many cases, the nucleic acid is then attached to a solid surface soas to preserve phase information subsequent to cleavage of the nucleicacid molecule. Preferably, the nucleic acid molecule is assembled invitro with nucleic acid-binding proteins to generate reconstitutedchromatin, though other suitable solid surfaces include nucleicacid-binding protein aggregates, nanoparticles, nucleic acid-bindingbeads, or beads coated using a nucleic acid-binding substance, polymers,synthetic nucleic acid-binding molecules, or other solid orsubstantially solid affinity molecules. A nucleic acid sample can alsobe obtained already attached to a solid surface, such as in the case ofnative chromatin. Native chromatin can be obtained having already beenfixed, such as in the form of a formalin-fixed paraffin-embedded (FFPE)or similarly preserved sample.

Following attachment to a nucleic acid binding moiety, the bound nucleicacid molecule can be cleaved. Cleavage is performed with any suitablenucleic acid cleavage entity, including any number of enzymatic andnon-enzymatic approaches. Preferably, DNA cleavage is performed with arestriction endonuclease, fragmentase, or transposase. Alternatively oradditionally, nucleic acid cleavage is achieved with other restrictionenzymes, topoisomerase, non-specific endonuclease, nucleic acid repairenzyme, RNA-guided nuclease, or alternate enzyme. Physical means canalso be used to generate cleavage, including mechanical means (e.g.,sonication, shear), thermal means (e.g., temperature change), orelectromagnetic means (e.g., irradiation, such as UV irradiation).Nucleic acid cleavage produces free nucleic acid ends, either having‘sticky’ overhangs or blunt ends, depending on the cleavage method used.When sticky overhang ends are generated, the sticky ends are optionallypartially filled in to prevent re-ligation. Alternatively, the overhangsare completely filled in to produce blunt ends.

In many cases, overhang ends are partially or completely filled in withdNTPs, which are optionally labeled. In such cases, dNTPs can bebiotinylated, sulphated, attached to a fluorophore, dephosphorylated, orany other number of nucleotide modifications. Nucleotide modificationscan also include epigenetic modifications, such as methylation (e.g.,5-mC, 5-hmC, 5-fC, 5-caC, 4-mC, 6-mA, 8-oxoG, 8-oxoA). Labels ormodifications can be selected from those detectable during sequencing,such as epigenetic modifications detectable by nanopore sequencing; inthis way, the locations of ligation junctions can be detected duringsequencing. These labels or modifications can also be targeted forbinding or enrichment; for example, antibodies targeting methyl-cytosinecan be used to capture, target, bind, or label blunt ends filled in withmethyl-cytosine. Non-natural nucleotides, non-canonical or modifiednucleotides, and nucleic acid analogs can also be used to label thelocations of blunt-end fill-in. Non-canonical or modified nucleotidescan include pseudouridine (Ψ), dihydrouridine (D), inosine (I),7-methylguanosine (m7G), xanthine, hypoxanthine, purine,2,6-diaminopurine, and 6,8-diaminopurine. Nucleic acid analogs caninclude peptide nucleic acid (PNA), Morpholino and locked nucleic acid(LNA), glycol nucleic acid (GNA), and threose nucleic acid (TNA). Insome cases, overhangs are filled in with un-labeled dNTPs, such as dNTPswithout biotin. In some cases, such as cleavage with a transposon, bluntends are generated that do not require filling in. These free blunt endsare generated when the transposase inserts two unlinked punctuationoligonucleotides. The punctuation oligonucleotides, however, aresynthesized to have sticky or blunt ends as desired. Proteins associatedwith sample nucleic acids, such as histones, can also be modified. Forexample, histones can be acetylated (e.g., at lysine residues) and/ormethylated (e.g., at lysine and arginine residues).

Next, while the cleaved nucleic acid molecule is still bound to thesolid surface, the free nucleic acid ends are linked together. Linkingoccurs, in some cases, through ligation, either between free ends, orwith a separate entity, such as an oligonucleotide. In some cases, theoligonucleotide is a punctuation oligonucleotide. In such cases, thepunctuation molecule ends are compatible with the free ends of thecleaved nucleic acid molecule. In many cases, the punctuation moleculeis dephosphorylated to prevent concatemerization of theoligonucleotides. In most cases, the punctuation molecule is ligated oneach end to a free nucleic acid end of the cleaved nucleic acidmolecule. In many cases, this ligation step results in rearrangements ofthe cleaved nucleic acid molecule such that two free ends that were notoriginally adjacent to one another in the starting nucleic acid moleculeare now linked in a paired end.

Following linking of the free ends of the cleaved nucleic acid molecule,the rearranged nucleic acid sample is released from the nucleic acidbinding moiety using any number of standard enzymatic and non-enzymaticapproaches. For example, in the case of in vitro reconstitutedchromatin, the rearranged nucleic acid molecule is released bydenaturing or degradation of the nucleic acid-binding proteins. In otherexamples, cross-linking is reversed. In yet other examples, affinityinteractions are reversed or blocked. The released nucleic acid moleculeis rearranged compared to the input nucleic acid molecule. In caseswhere punctuation molecules are used, the resulting rearranged moleculeis referred to as a punctuated molecule due to the punctuationoligonucleotides that are interspersed throughout the rearranged nucleicacid molecule. In these cases, the nucleic acid segments flanking thepunctuations make up a paired end.

During the cleavage and linking steps of the methods disclosed herein,phase information is maintained since the nucleic acid molecule is boundto a solid surface throughout these processes. This can enable theanalysis of phase information without relying on information from othermarkers, such as single nucleotide polymorphisms (SNPs). Using themethods and compositions disclosed herein, in some cases, two nucleicacid segments within the nucleic acid molecule are rearranged such thatthey are closer in proximity than they were on the original nucleic acidmolecule. In many examples, the original separation distance of the twonucleic acid segments in the starting nucleic acid sample is greaterthan the average read length of standard sequencing technologies. Forexample, the starting separation distance between the two nucleic acidsegments within the input nucleic acid sample is about 10 kb, 12.5 kb,15 kb, 17.5 kb, 20 kb, 25 kb, 30 kb, 35 kb, 40 kb, 45 kb, 50 kb, 60 kb,70 kb, 80 kb, 90 kb, 100 kb, 125 kb, 150 kb, 200 kb, 300 kb, 400 kb, 500kb, 600 kb, 700 kb, 800 kb, 900 kb, 1 Mb, or greater. In preferredexamples, the separation distance between the two rearranged DNAsegments is less than the average read length of standard sequencingtechnologies. For example, the distance separating the two rearrangedDNA segments within the rearranged DNA molecule is less than about 50kb, 40 kb, 30 kb, 25 kb, 20 kb, 17 kb, 15 kb, 14 kb, 13 kb, 12 kb, 11kb, 10 kb, 9 kb, 8 kb, 7 kb, 6 kb, 5 kb, or less. In preferred cases,the separation distance is less than that of the average read length ofa long-read sequencing machine. In these cases, when the rearranged DNAsample is released from the nucleic acid binding moiety and sequenced,phase information is determined and sequence information is generatedsufficient to generate a de novo sequence scaffold.

Barcoding a Rearranged Nucleic Acid Molecule

In some examples, the released rearranged nucleic acid moleculedescribed herein is further processed prior to sequencing. For example,the nucleic acid segments comprised within the rearranged nucleic acidmolecule can be barcoded. Barcoding can allow for easier grouping ofsequence reads. For example, barcodes can be used to identify sequencesoriginating from the same rearranged nucleic acid molecule. Barcodes canalso be used to uniquely identify individual junctions. For example,each junction can be marked with a unique (e.g., randomly generated)barcode which can uniquely identify the junction. Multiple barcodes canbe used together, such as a first barcode to identify sequencesoriginating from the same rearranged nucleic acid molecule and a secondbarcode that uniquely identifies individual junctions.

Barcoding can be achieved through a number of techniques. In some cases,barcodes can be included as a sequence within a punctuation oligo. Inother cases, the released rearranged nucleic acid molecule can becontacted to oligonucleotides comprising at least two segments: onesegment contains a barcode and a second segment contains a sequencecomplementary to a punctuation sequence. After annealing to thepunctuation sequences, the barcoded oligonucleotides are extended withpolymerase to yield barcoded molecules from the same punctuated nucleicacid molecule. Since the punctuated nucleic acid molecule is arearranged version of the input nucleic acid molecule, in which phaseinformation is preserved, the generated barcoded molecules are also fromthe same input nucleic acid molecule. These barcoded molecules comprisea barcode sequence, the punctuation complementary sequence, and genomicsequence.

For rearranged nucleic acid molecules with or without punctuation,molecules can be barcoded by other means. For example, rearrangednucleic acid molecules can be contacted with barcoded oligonucleotideswhich can be extended to incorporate sequence from the rearrangednucleic acid molecule. Barcodes can hybridize to punctuation sequences,to restriction enzyme recognition sites, to sites of interest (e.g.,genomic regions of interest), or to random sites (e.g., through a randomn-mer sequence on the barcode oligonucleotide). Rearranged nucleic acidmolecules can be contacted to the barcodes using appropriateconcentrations and/or separations (e.g., spatial or temporal separation)from other rearranged nucleic acid molecules in the sample such thatmultiple rearranged nucleic acid molecules are not given then samebarcode sequence. For example, a solution comprising rearranged nucleicacid molecules can be diluted to such a concentration that only onerearranged nucleic acid molecule will be contacted to a barcode or groupof barcodes with a given barcode sequence. Barcodes can be contacted torearranged nucleic acid molecules in free solution, in fluidicpartitions (e.g., droplets or wells), or on an array (e.g., atparticular array spots).

Barcoded nucleic acid molecules (e.g., extension products) can besequenced, for example, on a short-read sequencing machine and phaseinformation is determined by grouping sequence reads having the samebarcode into a common phase. Alternatively, prior to sequencing, thebarcoded products can be linked together, for example though bulkligation, to generate long molecules which are sequenced, for example,using long-read sequencing technology. In these cases, the embedded readpairs are identifiable via the amplification adapters and punctuationsequences. Further phase information is obtained from the barcodesequence of the read pair.

Determining Phase Information with Paired Ends

Further provided herein are methods and compositions for determiningphase information from paired ends. Paired ends can be generated by anyof the methods disclosed or those further illustrated in the providedExamples. For example, in the case of a nucleic acid molecule bound to asolid surface which was subsequently cleaved, following re-ligation offree ends, re-ligated nucleic acid segments are released from thesolid-phase attached nucleic acid molecule, for example, by restrictiondigestion. This release results in a plurality of paired ends. In somecases, the paired ends are ligated to amplification adapters, amplified,and sequenced with short reach technology. In these cases, paired endsfrom multiple different nucleic acid binding moiety-bound nucleic acidmolecules are within the sequenced sample. However, it is confidentlyconcluded that for either side of a paired end junction, the junctionadjacent sequence is derived from a common phase of a common molecule.In cases where paired ends are linked with a punctuationoligonucleotide, the paired end junction in the sequencing read isidentified by the punctuation oligonucleotide sequence. In other cases,the pair ends were linked by modified nucleotides, which can beidentified based on the sequence of the modified nucleotides used.

Alternatively, following release of paired ends, the free paired endscan be ligated to amplification adapters and amplified. In these cases,the plurality of paired ends is then bulk ligated together to generatelong molecules which are read using long-read sequencing technology. Inother examples, released paired ends are bulk ligated to each otherwithout the intervening amplification step. In either case, the embeddedread pairs are identifiable via the native DNA sequence adjacent to thelinking sequence, such as a punctuation sequence or modifiednucleotides. The concatenated paired ends are read on a long-sequencedevice, and sequence information for multiple junctions is obtained.Since the paired ends derived from multiple different nucleic acidbinding moiety-bound DNA molecules, sequences spanning two individualpaired ends, such as those flanking amplification adapter sequences, arefound to map to multiple different DNA molecules. However, it isconfidently concluded that for either side of a paired end junction, thejunction-adjacent sequence is derived from a common phase of a commonmolecule. For example, in the case of paired ends derived from apunctuated molecule, sequences flanking the punctuation sequence areconfidently assigned to a common DNA molecule. In preferred cases,because the individual paired ends are concatenated using the methodsand compositions disclosed herein, one can sequence multiple paired endsin a single read.

Sequencing Approaches

The methods and compositions disclosed herein can be used to generatelong DNA molecules comprising rearranged segments compared to the inputDNA sample. These molecules are sequences using any number of sequencingtechnologies. Preferably, the long molecules are sequenced usingstandard long-read sequencing technologies. Additionally oralternatively, the generated long molecules can be modified as disclosedherein to make them compatible with short-read sequencing technologies.

Exemplary long-read sequencing technologies include but are not limitedto nanopore sequencing technologies and other long-read sequencingtechnologies such as Pacific Biosciences Single Molecule Real Time(SMRT) sequencing. Nanopore sequencing technologies include but are notlimited to Oxford Nanopore sequencing technologies (e.g., GridION,MinION) and Genia sequencing technologies.

Sequence read lengths can be at least about 100 bp, 200 bp, 300 bp, 400bp, 500 bp, 600 bp, 700 bp, 800 bp, 900 bp, 1 kb, 2 kb, 3 kb, 4 kb, 5kb, 6 kb, 7 kb, 8 kb, 9 kb, 10 kb, 20 kb, 30 kb, 40 kb, 50 kb, 60 kb, 70kb, 80 kb, 90 kb, 100 kb, 200 kb, 300 kb, 400 kb, 500 kb, 600 kb, 700kb, 800 kb, 900 kb, 1 Mb, 2 Mb, 3 Mb, 4 Mb, 5 Mb, 6 Mb, 7 Mb, 8 Mb, 9Mb, or 10 Mb. Sequence read lengths can be about 100 bp, 200 bp, 300 bp,400 bp, 500 bp, 600 bp, 700 bp, 800 bp, 900 bp, 1 kb, 2 kb, 3 kb, 4 kb,5 kb, 6 kb, 7 kb, 8 kb, 9 kb, 10 kb, 20 kb, 30 kb, 40 kb, 50 kb, 60 kb,70 kb, 80 kb, 90 kb, 100 kb, 200 kb, 300 kb, 400 kb, 500 kb, 600 kb, 700kb, 800 kb, 900 kb, 1 Mb, 2 Mb, 3 Mb, 4 Mb, 5 Mb, 6 Mb, 7 Mb, 8 Mb, 9Mb, or 10 Mb. In some cases, sequence read lengths are at least about 5kb. In some cases, sequence read lengths are about 5 kb.

In some examples, a long rearranged DNA molecule generated using themethods and compositions disclosed herein, is ligated on one end to asequencing adapter. In preferred examples, the sequencing adapter is ahairpin adapter, resulting in a self-annealing single-stranded moleculeharboring an inverted repeat. In these cases, the molecule is fedthrough a sequencing enzyme and full length sequence of each side of theinverted repeat is obtained. In most cases, the resulting sequence readcorresponds to 2× coverage of the DNA molecule, such as a punctuated DNAmolecule harboring multiple rearranged segments, each conveying phaseinformation. In favored instances, sufficient sequence is generated toindependently generate a de novo scaffold of the nucleic acid sample.

Alternatively, a long rearranged DNA molecule generated using themethods and compositions disclosed herein, is cleaved to form apopulation of double stranded molecules of a desired length. In thesecases, these molecules are ligated on each end to single strandedadapters. The result is a double stranded DNA template capped by hairpinloops at both ends. The circular molecules are sequenced by continuoussequencing technology. Continuous long read sequencing of moleculescontaining a long double stranded segment results in a single contiguousread of each molecule. Continuous sequencing of molecules containing ashort double stranded segment results in multiple reads of the molecule,which are used either alone or along with continuous long read sequenceinformation to confirm a consensus sequence of the molecule. In mostcases, genomic segment borders marked by punctuation oligonucleotidesare identified, and it is concluded that sequence adjacent to apunctuation border is in phase. In preferred cases, sufficient sequenceis generated to independently generate a de novo scaffold of the nucleicacid sample.

In some cases, rearranged nucleic acid molecules are selected forsequencing based on length. Length-based selection can be used to selectfor rearranged nucleic acid molecules that contain more rearrangedsegments, so that shorter rearranged nucleic acid molecules containingonly a few rearranged segments are not sequenced or are sequenced infewer numbers. Rearranged nucleic acid molecules containing morerearranged segments can provide more phasing information than thosemolecules containing fewer rearranged segments. Rearranged nucleic acidmolecules can be selected for those that contain at least 1, 2, 3, 4, 5,6, 7, 8, 9, 10, or more rearranged segments. For example, rearrangednucleic acid molecules can be selected for a length of at least 100 bp,200 bp, 300 bp, 400 bp, 500 bp, 600 bp, 700 bp, 800 bp, 900 bp, 1 kb, 2kb, 3 kb, 4 kb, 5 kb, 6 kb, 7 kb, 8 kb, 9 kb, 10 kb, 20 kb, 30 kb, 40kb, 50 kb, 60 kb, 70 kb, 80 kb, 90 kb, 100 kb, 200 kb, 300 kb, 400 kb,500 kb, 600 kb, 700 kb, 800 kb, 900 kb, 1 Mb, 2 Mb, 3 Mb, 4 Mb, 5 Mb, 6Mb, 7 Mb, 8 Mb, 9 Mb, 10 Mb, or more. Length-based selection can be afirm exclusion, excluding 100% of rearranged nucleic acid moleculesbelow the chosen length. Alternatively, length-based selection can be anenrichment for longer molecules, removing at least 99.999%, 99.99%,99.9%, 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 85%, 80%, 75%,70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, 4%,3%, 2%, or 1% of rearranged nucleic acid molecules below the chosenlength. Length selection of nucleic acids can be performed by a varietyof techniques, including but not limited to electrophoresis (e.g., gelor capillary), filtration, bead binding (e.g., SPRI bead sizeselection), and flow-based methods.

Phased Sequence Assembly

Sequencing data generated using the methods and compositions describedherein are used, in preferred embodiments, to generate phased de novosequence assemblies.

In some examples, a plurality of rearranged (and optionally punctuated)DNA molecules are generated as disclosed herein, and subsequentlysequenced using long-read sequencing technology. Sequences from theplurality of rearranged (and optionally punctuated) DNA molecules arecompared and, in many cases, a first rearranged (and optionallypunctuated) molecule is used to determine phase information for itsconstituent segments, while comparison to un-rearranged (and optionallypunctuated) regions of a second (and additional) rearranged (andoptionally punctuated) DNA molecules is used to order the segments ofthe first punctuated molecule. Repeating this process reciprocally,phase and order information is determined for the majority of thesegments in each of the plurality of rearranged molecules. In preferredcases, the resulting assembled sequence is a phased sequence of theinput DNA molecule prior to rearrangement occurring, and represents a denovo, phased assembly of the nucleic acid sample.

Alternatively, a rearranged DNA molecule as generated using the methodsand compositions disclosed herein is sequenced using long-readsequencing technology and, in parallel, the input DNA is sequenced usingstandard short-read shotgun sequencing technology. In these cases, theshotgun sequence from the sample is mapped to the long read datagenerated from the rearranged DNA molecule and/or the phased genomicsequence reads from the rearranged molecule are mapped to sequencingdata obtained from the concurrently generated short-read sequencing. Insome cases, some of the short-reads map to the long-read generatedsequence. In such cases, this overlap allows short sequence reads to beassigned to the same phase as the genomic sequence generated from therearranged DNA molecule long sequence read.

Information irrelevant to generating a phased sequence assembly can bediscarded. In an example, a rearranged DNA molecule as discussed hereinis generated and sequenced. The rearranged DNA molecule is found tocomprise segments that map to chromosome A and segments that map tochromosome B. In some cases, sequence read information for segments thatmap to chromosome B can be discarded or unused, and only segments thatmap to chromosome A are used to generate phased sequence information. Inother cases, sequence read information for segments that map tochromosome A can be used to generate phased sequence information aboutchromosome A, while sequence read information for segments that map tochromosome B can be used to generate phased sequence information aboutchromosome B, but information about the junction(s) between chromosome Asegments and chromosome B segments remains unused or is discarded.

Samples can be manipulated to reduce or remove inter-chromosomalproximity or junction information. For example, a cell sample can befrozen in mitosis prior to rearrangement and sequencing as describedherein, thereby disrupting the usual three-dimensional structure ofchromosomes in the cells. This can reduce or eliminate inter-chromosomalligations. In another example, histone post-translational modificationscan be removed prior to analysis.

Nucleic Acid Sequence Libraries

Also disclosed herein are methods and compositions for generatingnucleic acid sequence libraries. Rearranged molecules are sequenced, andthe sequence reads are analyzed. For a given read, sequence segments canbe observed and parsed into multiple rearranged segments. If punctuationoligos are employed, sequence segments can be observed that are locallyuninterrupted by punctuation elements. Sequence information in sequencesegments is presumed to be in phase, and locally correctly ordered andoriented. Segments on either side of a junction are inferred to be inphase with one another on a common sample nucleic acid molecule but notnecessarily to be correctly ordered and oriented relative to one anotheron the rearranged nucleic acid molecule. A benefit of the rearrangementis that segments positioned far removed from one another are sometimesbrought into proximity, such that they are read in a common read andconfidently assigned to a common phase even if in the sample moleculethey are separated by large distances of identical, difficult to phasesequence. Another benefit is that the segment sequences themselvescomprise most, substantially all or all of the original sample sequence,such that in addition to phase information, in some cases contiginformation is determined sufficient to perform de novo sequenceassembly in some cases. This de novo sequence is optionally used togenerate a novel scaffold or contig set, or to augment a previously orindependently generated contig or scaffold sequence set.

Rearranged molecules, such as in a sequencing library, can comprise atleast 2, 3, 4, 5, 6, 7, 8, 9, 10, or more segments, where the segmentsare not adjacent to other segments on the original input nucleic acidmolecule (e.g., input genomic DNA). In some cases, at least about 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%,99.99%, 99.999%, or 100% of the segments on a given rearranged moleculemap to a common scaffold. In some cases, on average over a population ofrearranged molecules such as a sequencing library, at least about 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%,99.99%, 99.999%, or 100% of the segments on a given rearranged moleculemap to a common scaffold.

Segments can be about 100 bp, 200 bp, 300 bp, 400 bp, 500 bp, 600 bp,700 bp, 800 bp, 900 bp, 1 kb, 1.1 kb, 1.2 kb, 1.3 kb, 1.4 kb, 1.5 kb,2.0 kb, 2.5 kb, 3.0 kb, 3.5 kb, 4.0 kb, 4.5 kb, 5.0 kb, 5.5 kb, 6.0 kb,6.5 kb, 7.0 kb, 7.5 kb, 8.0 kb, 8.5 kb, 9.0 kb, 9.5 kb, 10.0 kb, orgreater in length. Segments can be at least about 100 bp, 200 bp, 300bp, 400 bp, 500 bp, 600 bp, 700 bp, 800 bp, 900 bp, 1 kb, 1.1 kb, 1.2kb, 1.3 kb, 1.4 kb, 1.5 kb, 2.0 kb, 2.5 kb, 3.0 kb, 3.5 kb, 4.0 kb, 4.5kb, 5.0 kb, 5.5 kb, 6.0 kb, 6.5 kb, 7.0 kb, 7.5 kb, 8.0 kb, 8.5 kb, 9.0kb, 9.5 kb, 10.0 kb, or greater in length. Segments can be at most about100 bp, 200 bp, 300 bp, 400 bp, 500 bp, 600 bp, 700 bp, 800 bp, 900 bp,1 kb, 1.1 kb, 1.2 kb, 1.3 kb, 1.4 kb, 1.5 kb, 2.0 kb, 2.5 kb, 3.0 kb,3.5 kb, 4.0 kb, 4.5 kb, 5.0 kb, 5.5 kb, 6.0 kb, 6.5 kb, 7.0 kb, 7.5 kb,8.0 kb, 8.5 kb, 9.0 kb, 9.5 kb, 10.0 kb, or greater in length.

Rearranged molecules can have at least 2, 3, 4, 5, 6, 7, 8, 9, 10, ormore segments that are at least about 100 bp, 200 bp, 300 bp, 400 bp,500 bp, 600 bp, 700 bp, 800 bp, 900 bp, 1 kb, 1.1 kb, 1.2 kb, 1.3 kb,1.4 kb, 1.5 kb, 2.0 kb, 2.5 kb, 3.0 kb, 3.5 kb, 4.0 kb, 4.5 kb, 5.0 kb,5.5 kb, 6.0 kb, 6.5 kb, 7.0 kb, 7.5 kb, 8.0 kb, 8.5 kb, 9.0 kb, 9.5 kb,10.0 kb, or greater in length. In some cases, rearranged molecules haveat least 3 segments that are at least 500 bp in length. In some cases,rearranged molecules have at least 4 segments that are at least 500 bpin length. In some cases, rearranged molecules have at least 5 segmentsthat are at least 500 bp in length. In some cases, rearranged moleculeshave at least 6 segments that are at least 500 bp in length.

Rearranged molecules can comprise, when added up across all segments inthe rearranged molecule, at least 100 bp, 200 bp, 300 bp, 400 bp, 500bp, 600 bp, 700 bp, 800 bp, 900 bp, 1 kb, 1.1 kb, 1.2 kb, 1.3 kb, 1.4kb, 1.5 kb, 2.0 kb, 2.5 kb, 3.0 kb, 3.5 kb, 4.0 kb, 4.5 kb, 5.0 kb, 5.5kb, 6.0 kb, 6.5 kb, 7.0 kb, 7.5 kb, 8.0 kb, 8.5 kb, 9.0 kb, 9.5 kb, 10.0kb from one original nucleic acid molecule (e.g, from one chromosome).In some cases, rearranged molecules comprise, when added up across allsegments in the rearranged molecule, at least 1000 bp from one originalnucleic acid molecule (e.g., from one chromosome). In some cases,rearranged molecules comprise, when added up across all segments in therearranged molecule, at least 2000 bp from one original nucleic acidmolecule (e.g., from one chromosome). In some cases, rearrangedmolecules comprise, when added up across all segments in the rearrangedmolecule, at least 3000 bp from one original nucleic acid molecule(e.g., from one chromosome). In some cases, rearranged moleculescomprise, when added up across all segments in the rearranged molecule,at least 4000 bp from one original nucleic acid molecule (e.g., from onechromosome). In some cases, rearranged molecules comprise, when added upacross all segments in the rearranged molecule, at least 5000 bp fromone original nucleic acid molecule (e.g., from one chromosome).

In some cases, mapping can be conducted with enforced unique mapping. Insome cases, less than about 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%,5%, 4%, 3%, 2%, 1%, 0.1%, 0.01%, or 0.001% of segments map ambiguously(e.g., map to multiple locations).

A sequencing library can comprise at least about 10, 100, 1000, 10,000,100,000, 1 million, 1.1 million, 1.2 million, 1.3 million, 1.4 million,1.5 million, 1.6 million, 1.7 million, 1.8 million, 1.9 million, 2.0million, 3 million, 4 million, 5 million, 6 million, 7 million, 8million, 9 million, 10 million, 20 million, 30 million, 40 million, 50million, 60 million, 70 million, 80 million, 90 million, 100 million,200 million, 300 million, 400 million, 500 million, 600 million, 700million, 800 million, 900 million, 1 billion, 2 billion, 3 billion, 4billion, 5 billion, 6 billion, 7 billion, 8 billion, 9 billion, 10billion, 100 billion, 200 billion, 300 billion, 400 billion, 500billion, 600 billion, 700 billion, 800 billion, 900 billion, or 1trillion rearranged molecules.

Rearranged molecules in a sequencing library can comprise the necessaryadapters, labels, or other components for sequencing, such as particularrecognition sequences, hybridization sequences, hairpins (e.g., forSMRTbell), tags (e.g., NanoTags), labels, dyes, or barcodes.

In some cases, a plurality of rearranged DNA molecules is generated asdisclosed herein and subsequently sequenced using long-read sequencingtechnology. Each rearranged molecule is sequenced, and the sequencereads are analyzed. In preferred examples, sequence reads average atleast about 5 kb or at least about 10 kb for the sequence reaction. Inother examples, sequence reads average at least about 5 kb, 6 kb, 7 kb,8 kb, 9 kb, 10 kb, 11 kb, 12 kb, 13 kb, 14 kb, 15 kb, 16 kb, 17 kb, 18kb, 19 kb, 20 kb, 21 kb, 22 kb, 25 kb, 30 kb, 35 kb, 40 kb, or greater.In favored examples, sequence reads are identified that comprise atleast 500 bases of a first segment and 500 bases of a second segment,where the first and second segments are not adjacent on the originalsample input nucleic acid. The segments can be joined by a punctuationoligo sequence. In other examples, the sequence reads comprise at leastabout 100 bases, 200 bases, 300 bases, 400 bases, 500 bases, 600 bases,700 bases, 800 bases, 900 bases, 1000 bases, or greater of a first DNAsegment and at least about 100 bases, 200 bases, 300 bases, 400 bases,500 bases, 600 bases, 700 bases, 800 bases, 900 bases, 1000 bases, orgreater of a second DNA segment. In some examples, the first and secondsegment sequences are mapped to a scaffold genome and are found to mapto contigs that are separated by at least 100 kb. In other examples, theseparation distance is at least about 8 kb, 9 kb, 10 kb, 12.5 kb, 15 kb,17.5 kb, 20 kb, 25 kb, 30 kb, 35 kb, 40 kb, 45 kb, 50 kb, 60 kb, 70 kb,80 kb, 90 kb, 100 kb, 125 kb, 150 kb, 200 kb, 300 kb, 400 kb, 500 kb,600 kb, 700 kb, 800 kb, 900 kb, 1 Mb, or greater. In most cases, thefirst contig and the second contig each comprise a single heterozygousposition, the phase of which is not determined in a scaffold. Inpreferred examples, the heterozygous position of the first contig isspanned by the first segment of the long read, and the heterozygousposition of the second contig is spanned by the second segment of thelong read. In such cases, the reads each span their contigs' respectiveheterozygous regions and sequence of the read segments indicates that afirst allele of the first contig and a first allele of the second contigare in phase. If sequences from the first and second nucleic acidsegments are detected in a single long sequence read, it is determinedthat the first and second nucleic acid segments are comprised on thesame DNA molecule in the input DNA sample. In these preferredembodiments, nucleic acid sequence libraries generated by the methodsand compositions disclosed herein provide phase information for contigsthat are positioned far apart from one another on a genome scaffold.

Alternatively, a plurality of paired end molecules is generated asdescribed herein, and subsequently sequenced using long read sequencingtechnology. In some cases, the average read length for the library isdetermined to be about 1 kb. In other cases, the average read length forthe library is about 100 bp, 200 bp, 300 bp, 400 bp, 500 bp, 600 bp, 700bp, 800 bp, 900 bp, 1 kb, 1.1 kb, 1.2 kb, 1.3 kb, 1.4 kb, 1.5 kb, 2.0kb, 2.5 kb, 3.0 kb, 3.5 kb, 4.0 kb, 4.5 kb, 5.0 kb, 5.5 kb, 6.0 kb, 6.5kb, 7.0 kb, 7.5 kb, 8.0 kb, 8.5 kb, 9.0 kb, 9.5 kb, 10.0 kb, or greater.In many examples, paired end molecules comprise a first DNA segment anda second DNA segment that, within the input DNA sample, are in phase andseparated by a distance greater than 10 kb. In some examples, theseparation distance between two such DNA segments is greater than about5 kb, 6 kb, 7 kb, 8 kb, 9 kb, 10 kb, 11 kb, 12 kb, 13 kb, 14 kb, 15 kb,20 kb, 23 kb, 25 kb, 30 kb, 32 kb, 35 kb, 40 kb, 50 kb, 60 kb, 75 kb,100 kb, 200 kb, 300 kb, 400 kb, 500 kb, 750 kb, 1 Mb, or greater. Inmost cases, sequence reads are generated from paired end molecules, someof which comprise at least 300 bases of sequence from a first nucleicacid segment and at least 300 bases of sequence from a second nucleicacid segment. In other examples, the sequence reads comprise at leastabout 50 bases, 100 bases, 150 bases, 200 bases, 250 bases, 300 bases,350 bases, 400 bases, 450 bases, 500 bases, 550 bases, 600 bases, 650bases, 700 bases, 750 bases, 800 bases, or greater of a first DNAsegment and at least about 50 bases, 100 bases, 150 bases, 200 bases,250 bases, 300 bases, 350 bases, 400 bases, 450 bases, 500 bases, 550bases, 600 bases, 650 bases, 700 bases, 750 bases, 800 bases, or greaterof a second DNA segment. If sequences from the first and second nucleicacid segments are detected in a single sequence read, it can bedetermined that the first and second nucleic acid segments are in phaseon the same DNA molecule in the input DNA sample. In such cases, thegenerated sequence libraries yield phase information for DNA segmentsthat are separated in the nucleic acid sample by greater than the readlength of the sequencing technology used to sequence them.

Alternatively, a plurality of sequence reads is generated from arearranged DNA nucleic acid sequence library as discloses herein. Insome cases, the library conveys phase information, as disclosed hereinand as described in the provided Examples, such that segments on eitherside of a segment junction are determined to be in phase on a singlemolecule. In some examples, the generated sequence reads represent atleast 80% of the nucleic acid sequence of the input DNA sample. In otherexamples, the generated sequence reads represent at least about 45%,50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% of the nucleicacid sequence of the input DNA sample. In preferred examples, thesequence reads are used to generate de novo contig information thatspans at least 80% of the input DNA sample. In other examples, thesequence reads are used to generate de novo contig information thatspans at least about 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, or 100% of the input DNA sample. In most cases, the sequence readsare used to determine phase information, which is optionallysubsequently used to order and orient the contigs relative to each otherin order to generate a phased sequence assembly of the input DNA sample.In preferred embodiments, the nucleic acid sequence libraries generatedfrom the rearranged DNA molecules convey phase information and,preferably, also encompass sequence information comprising a substantialportion of the total nucleic acid sequence, such that a de novo sequenceassembly is concurrently generated.

Sequencing of a library of rearranged molecules can be performed toachieve a sequencing coverage of at least about 1×, 2×, 3×, 4×, 5×, 6×,7×, 8×, 9×, 10, 11×, 12×, 13×, 14×, 15×, 16×, 17×, 18×, 19×, 20×, 21×,22×, 23×, 24×, 25×, 26×, 27×, 28×, 29×, 30×, 31×, 32×, 33×, 34×, 35×,336×, 37×, 38×, 39×, 40×, 41×, 42×, 43×, 44×, 45×, 46×, 47×, 48×, 49×,50×, 55×, 60×, 65×, 70×, 75×, 80×, 85×, 90×, 95×, 100×, or more.

Preserved DNA Molecule Phasing

Furthermore, disclosed herein are methods and compositions for phasingand de novo assembling a nucleic acid sequence that, in preferredembodiments, comprises nearly the entire input nucleic acid molecule.

The techniques of the present disclosure can be used to phase a varietyof markers, including but not limited to single nucleotide polymorphisms(SNPs), insertions or deletions (INDELs), and structural variants (SVs).For example, the presence of two or more segments together on arearranged DNA molecule can be used to infer that the sequences of thesegments are in phase. This can permit phasing without reliance onpreviously known phasing of markers. In some cases, SNPs are phased. Insome cases, INDELs are phased. In some cases, SVs are phased. Phasingcan be confirmed with reference to one or more markers. In some cases,phasing is confirmed with reference to SNPs. In some cases, phasing isconfirmed without reference to SNPs. In some cases, phasing is confirmedwith reference to INDELs. In some cases, phasing is confirmed withoutreference to INDELs. In some cases, phasing is confirmed with referenceto SVs. In some cases, phasing is confirmed without reference to SVs. Insome examples, a high molecular weight (HMW) nucleic acid sample isextracted using standard methods known in the art. In most cases, theseHMW nucleic acid samples comprise at least some nucleic acid moleculeswhich are at least 100 kb in length. One or more of the 100 kb nucleicacid molecules comprises a first nucleic acid segment and a secondnucleic acid segment that are separated by distance that is greater thanthe average read length of standard sequencing technologies. In otherexamples, the nucleic acid sample comprises at least some nucleic acidmolecules which are at least about 30 kb, 40 kb, 50 kb, 60 kb, 70 kb, 80kb, 90 kb, 100 kb, 110 kb, 120 kb, 130 kb, 140 kb, 150 kb, or greater inlength, one or more of which comprises at least a first nucleic acidsegment and a second nucleic acid segment that are separated by adistance that is greater than the average read length of standardsequencing technologies, such as those described herein.

To determine the phase information is such examples, the first andsecond nucleic acid segments need to be detected within a singlesequencing read. Therefore, the relative position of the first andsecond nucleic acid segments must be changed such that the first andsecond DNA segments are separated by a distance that is less than theaverage read length of standard sequencing technologies. In order togenerate the desired phase information, this rearrangement should notresult in loss of phase information. In preferred examples, thisrearrangement is achieved by the methods and compositions disclosedherein and as described within the provided Examples. In favoredexamples, during phase-maintaining rearrangement, no more than 10% ofthe starting nucleic acid molecule is deleted. That is, the firstsegment and the second segment are not brought into proximity simply bydeleting the intervening sequence. Rather, the segments are rearrangedrelative to one another without deletion of the majority of theintervening sequence. In other examples, no more than about 2%, 5%, 7%,10%, 12%, 13%, 14%, 15%, 20%, 23%, 25%, 30%, 35%, 40%, 50%, 55%, 60%,70%, 80%, 90%, or 95% of the starting nucleic acid molecule is deleted.Since, in favored examples, nearly the entire input nucleic acidmolecule is preserved, following sequencing, the generated sequencereads are used to assemble, order, and orient de novo generated contigssuch that nearly the entire input nucleic acid molecule is sequenced,assembled, and phased.

Applications

The techniques of the present disclosure can be used for a variety ofgenetics and genomics applications, including but not limited togeneration of de novo sequence assemblies (including phased sequenceassemblies), mapping reads to a scaffold (including with phasinginformation), determining phasing information, and identifyingstructural variants.

The techniques disclosed herein are useful in many fields including, byway of non-limiting example, forensics, agriculture, environmentalstudies, renewable energy, epidemiology or disease outbreak response,and species preservation.

Techniques of the present disclosure can be used for diagnosing diseasestates, such as cancer. Techniques of the present disclosure can be usedfor phasing of clinically important regions, analysis of structuralvariants, resolution of pseudogenes (e.g., STRC), targeted panels fordrugable structural variants in cancer, and other applications. Forexample, an excess of proximity ligation evens between regions of thegenome that are far apart linearly or on separate chromosomes can beindicative of diseases like cancer.

Native chromatin from tissue that is diseased or suspected of beingdiseased can be analyzed using the techniques of the present disclosure.The three-dimensional architecture of the genome within such a tissuesample can be analyzed, for example by analyzing several samples fromdifferent locations within a tissue volume.

In some cases, such as for de novo genome assembly, the biological orpathological signal can be removed from these data. For example, cellscan be treated with reagents that cause mitotic arrest, or that disruptheterochromatin or other regional features of genome architecture, priorto adding a fixing agent that locks in the three-dimensionalarchitecture prior to proximity ligation. In such cases, the resultingdata can lack diagnostic utility, but can be maximally useful for genomeassembly.

Molecules and libraries generated as disclosed herein are used in anumber of applications, such as applications related to genome assemblyand contig or other sequence information phasing, such as is done toassign sequence information to a specific molecule of origin or sisterchromatid of origin in a diploid organism's genome assembly.

Molecules are sequenced, and contiguous segments are identified asmapping to consecutive bases of a common contig or scaffold. Junctionsbetween segments are identified as regions where bases cease to map toconsecutive bases of a common contig or scaffold. In some cases, nucleicacid sequence that maps to multiple regions of a genome (such asrepetitive sequence) is discarded. Alternately, particularly if one orboth ends of a repetitive sequence maps to a common scaffold and thedifference between sequence positions for the uniquely mapping sequenceat the ends of the repetitive sequence is consistent with the repetitiveregion being included in the scaffold, then a repetitive region isassigned to a common segment with its adjacent unique sequence.

In preferred embodiments, adjacent segments of a molecule or libraryconstituent as disclosed herein are assigned to a common phase of acommon molecule of the genome. That is, the contigs to which thesegments map are assigned to a common phase, and single nucleotidepolymorphisms, insertions, deletions, transversions, translocations orother nucleic acid features indicated by one or both segments areassigned to a common molecule.

Often, all or a majority of segments map to a common scaffold or contig,such that their coexistence on a single molecule of the library isindicative that single nucleotide polymorphisms, insertions, deletions,transversions, translocations or other nucleic acid features indicatedby one or both segments are assigned to a common molecule. In some casesat least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or more than 99% of the segments, or atleast 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94,95%, 96%, 97%, 98%, 99%, or more than 99% of the segments sequence, mapsto a common scaffold.

In some cases it is beneficial to enrich for molecule generation so asto ensure or increase the likelihood of segments ligating so as toreflect physical linkage or phase information, or so that ligatedsegments arise from a common physical molecule of origin. A number ofapproaches effect this goal.

As discussed herein, in some cases libraries are generated through thecleavage and re-ligation of isolated nucleic acid molecules onto whichchromatin or other nucleic acid binding moieties have been assembled. Byisolating the molecules, for example by separating them from nucleicacid binding proteins or other native chromatin constituents, one allowsindividual molecules to separate from one another. By binding theisolated nucleic acid molecules such that separate segments are heldtogether independent of their common phosphodiester backbones, the phaseinformation common to segments of a molecule of origin is preservedduring the process of cleavage and relegation such that a cleavedsegment is likely to rejoin to a second segment derived from a moleculeof origin common to the two segments. This frequency is increasedthrough any number of approaches, such as, for example, by dilutingmolecules prior to chromatin assembly, or by attaching nucleic acidmolecules to distinct locations on a common surface at a density belowthat at which segments form separate molecules are likely to ligate.When beads such as SPRI beads are used to anchor molecules for digestionand assembly, selecting beads that have larger surface areas, or addingmore beads so as to increase the total overall surface area availablefor binding, in some cases decreases the chance of intermolecularligation events.

Alternately, in some cases steps are taken to reduce intermolecularinteractions among nucleic acid molecules that are bound by nativechromatin, such as occurs when cells are treated using a fixative.Examples of such steps include actively targeting cells at a point intheir cell cycles such that intermolecular interactions are likely to beminimized. This is accomplished in some cases by freezing or fixingcells in mitosis so as to selectively access their nucleic acids whenchromosomes are less likely to be assembled into sub-nuclear structuresthat may lead to intermolecular ligation events. Alternately or incombination, cells, nuclei, or isolated chromatin from cells are treatedso as to remove histone post-translational modifications, so as toremove three-dimensional mapping information and concurrently improvethe chance that segments from a single molecule ligate to one another inlibrary generation for sequencing/phasing information.

Aside from biochemical or ‘wet-lab’ approaches to reducingintermolecular ligation events in rearranged library formation,computational approaches are also available to reduce the impact ofintermolecular ligation events on phase determination. For example, insome cases individual molecules are screened by assessing the mappingdistributions of uniquely mapping segments in ligated rearrangedmolecules. Molecules comprising segments that map to likely distinctmolecules above a threshold level are excluded. That is, in some cases,sequence information for molecules that comprise segments that uniquelymap to a common scaffold at less than 50%, 55%, 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%, or up to 99% or greater are excluded from furtheranalysis. In exemplary cases, this threshold is at or about 70%, or ator about 80%, or at or about 90%. In these cases, sequence of moleculesthat comprise a percentage of segments that map elsewhere than a firstcommon scaffold is excluded from analysis.

Similarly, in some cases, sequence information for molecules thatcomprise aggregate uniquely mapping sequence that map to a commonscaffold at less than 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%,or up to 99% or greater are excluded from further analysis. In exemplarycases, this threshold is at or about 70%, or at or about 80%, or at orabout 90%. In these cases, sequence of molecules that comprise apercentage of uniquely mapping sequence that map elsewhere than a firstcommon scaffold is excluded from analysis.

Alternately or in combination, sequences of molecules comprisingsegments that uniquely map to more than one scaffold are furtherprocessed, such as to minimize the impact on phase conclusions withoutlosing sequence information such as SNP data, insertion data, deletiondata, inversion data or other genomic rearrangement information that maybe captured in sequenced segments. For example, for molecule sequencesthat comprise segments that uniquely map to two scaffolds (predominantlyor exclusively), the segments that map to the first scaffold areassigned to a common phase of that scaffold, while the segments that mapto the second scaffold are assigned to a common phase of the secondscaffold. That is, segments that map to a first common scaffold areassigned to a common phase on that scaffold, while segments that map toa second common scaffold are determined to be informative of commonphase information for the second scaffold, but the segments that map(such as uniquely map) to the first scaffold are not determined to beinformative as to phase information with respect to the segments thatmap to the second scaffold.

Alternately, in some cases a plurality of independent molecule sequencesare obtained comprising first population of segments that uniquely mapto a first scaffold, and a second population of segments that uniquelymap to a second scaffold. In these cases, it is optionally inferred thatthe first scaffold and the second scaffold are in fact in phase in thenucleic acid sample, for example due to a translocation in the samplegenome under analysis.

These approaches allow for the selective enrichment for molecularsequence that is likely to be informative as to phase of the underlyingmolecules from which the rearranged library, and the rearrangedlibrary's sequence data, are derived.

In some cases library generation and sequence analysis are used incombination to obtain sequence information and phase information. Insome such cases, ligation junctions are labeled, for example using amodified nucleotide base that is compatible with long read sequencingtechnology and that is readily identified in reads of such technology.Examples are provided herein.

Using such junction markers, one is able to identify segment junctionswith a high degree of confidence independent of the segment sequence.Consequently, sequence rearrangements in library construction arereadily distinguished from ‘rearrangement events’ that occur in thesample and are reflective of sample nucleic acid sequence orarchitecture. Such events include, for example, insertions, deletions,inversions, transversions or translocations. Observing such events in asegment, when such events are not tagged by a junction marker such as amodified nucleic acid, is indicative that the events are reflective ofunderlying sample sequence.

Alternately or in combination, one may rely upon depth of librarycoverage to provide some degree of confidence as to molecular structure.That is, in sequencing multiple independently generated libraryconstituents, one may find multiple, independently generated segmentssharing a common rearrangement profile. If such profile comprises acommon ‘rearrangement event’ in multiple independently derived libraryconstituents, one may infer that the ‘rearrangement event’ which theyindicate is reflective of the underlying sample sequence rather thanbeing a product of the library generation process.

A wide diversity of library constituents are consistent with thedisclosure herein. Library constituents are preferably longer on averagethan a single read of prevailing long read sequencing technology, suchthat the sequencing technology is used most efficiently in sequencingthe library. However, this is not an absolute requirement, and librariescomprising, predominantly comprising, or consisting of constituentssmaller than the length of a long range sequencing run are consistentwith the disclosure herein.

Libraries disclosed herein may vary in their fraction of the overallsample represented in the library, mean or median rearranged moleculesize, segment size, and number of segments per molecule. In manyembodiments, libraries are configured so that a single long read spansat least part of three segments of a molecular constituent of thelibrary. In many embodiments, libraries are configured so that segmentsin phase but dispersed throughout a genomic sample are reconfigured sothat they are adjacent or otherwise included in a single long rangesequence read, so as to facilitate their assignment to a common phase ofa common molecule.

Computer Systems and Improvement in Operation Thereof

Methods as described herein are in some cases implemented by way ofmachine (or computer processor) executable code (or software) stored onan electronic storage location of the server 1001, such as, for example,on the memory 1010, or electronic storage unit 1015. During use, thecode can be executed by the processor 1005. In some cases, the code canbe retrieved from the storage unit 1015 and stored on the memory 1010for ready access by the processor 1005. In some situations, theelectronic storage unit 115 can be precluded, and machine-executableinstructions are stored on memory 1010. Alternatively, the code can beexecuted on a second computer system 1040.

Aspects of the systems and methods provided herein, such as the server1001, can be embodied in programming. Various aspects of the technologymay be thought of as “products” or “articles of manufacture” typicallyin the form of machine (or processor) executable code and/or associateddata that is carried on or embodied in a type of machine readablemedium. Machine-executable code can be stored on an electronic storageunit, such memory (for example, read-only memory, random-access memory,flash memory) or a hard disk. “Storage” type media can include any orall of the tangible memory of the computers, processors or the like, orassociated modules thereof, such as various semiconductor memories, tapedrives, disk drives and the like, which may provide non-transitorystorage at any time for the software programming. All or portions of thesoftware may at times be communicated through the Internet or variousother telecommunication networks. Such communications, for example, mayenable loading of the software from one computer or processor intoanother, for example, from a management server or host computer into thecomputer platform of an application server. Thus, another type of mediathat may bear the software elements includes optical, electrical, andelectromagnetic waves, such as used across physical interfaces betweenlocal devices, through wired and optical landline networks and overvarious air-links. The physical elements that carry such waves, such aswired or wireless likes, optical links, or the like, also may beconsidered as media bearing the software. As used herein, unlessrestricted to non-transitory, tangible “storage” media, terms such ascomputer or machine “readable medium” can refer to any medium thatparticipates in providing instructions to a processor for execution.

Hence, a machine readable medium, such as computer-executable code, maytake many forms, including but not limited to, tangible storage medium,a carrier wave medium, or physical transmission medium. Non-volatilestorage media can include, for example, optical or magnetic disks, suchas any of the storage devices in any computer(s) or the like, such maybe used to implement the system. Tangible transmission media caninclude: coaxial cables, copper wires, and fiber optics (including thewires that comprise a bus within a computer system). Carrier-wavetransmission media may take the form of electric or electromagneticsignals, or acoustic or light waves such as those generated during radiofrequency (RF) and infrared (IR) data communications. Common forms ofcomputer-readable media therefore include, for example: a floppy disk, aflexible disk, hard disk, magnetic tape, any other magnetic medium, aCD-ROM, DVD, DVD-ROM, any other optical medium, punch cards, paper tame,any other physical storage medium with patterns of holes, a RAM, a ROM,a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, acarrier wave transporting data or instructions, cables, or linkstransporting such carrier wave, or any other medium from which acomputer may read programming code and/or data. Many of these forms ofcomputer readable media may be involved in carrying one or moresequences of one or more instructions to a processor for execution.

A computer system may be used to implement one or more steps of a methoddescribed herein, including, for example, sample collection, sampleprocessing, sequence generation and sequence analysis.

A client-server and/or relational database architecture can be used inany of the methods described herein. In general, a client-serverarchitecture is a network architecture in which each computer or processon the network is either a client or a server. Server computers can bepowerful computers dedicated to managing disk drives (file servers),printers (print servers), or network traffic (network servers). Clientcomputers can include PCs (personal computers) or workstations on whichusers run applications, as well as example output devices as disclosedherein. Client computers can rely on server computers for resources,such as files, devices, and even processing power. The server computerhandles all of the database functionality. The client computer can havesoftware that handles front-end data management and receive data inputfrom users.

After performing a calculation, a processor can provide the output, suchas from a calculation, back to, for example, the input device or storageunit, to another storage unit of the same or different computer system,or to an output device. Output from the processor can be displayed by adata display, for example, a display screen (for example, a monitor or ascreen on a digital device), a print-out, a data signal (for example, apacket), a graphical user interface (for example, a webpage), an alarm(for example, a flashing light or a sound), or a combination of any ofthe above. In an embodiment, an output is transmitted over a network(for example, a wireless network) to an output device. The output devicecan be used by a user to receive the output from the data-processingcomputer system. After an output has been received by a user, the usercan determine a course of action, or can carry out a course of action,such as a medical treatment when the user is medical personnel. In someembodiments, an output device is the same device as the input device.Example output devices include, but are not limited to, a telephone, awireless telephone, a mobile phone, a PDA, a flash memory drive, a lightsource, a sound generator, a fax machine, a computer, a computermonitor, a printer, an iPod, and a webpage. The user station may be incommunication with a printer or a display monitor to output theinformation processed by the server. Such displays, output devices, anduser stations can be used to provide an alert to the subject or to acaregiver thereof.

Data relating to the present disclosure can be transmitted over anetwork or connections for reception and/or review by a receiver. Thereceiver can be but is not limited to the subject to whom the reportpertains; or to a caregiver thereof, for example, a health careprovider, manager, other healthcare professional, or other caretaker; aperson or entity that performed and/or ordered the genotyping analysis;a genetic counselor. The receiver can also be a local or remote systemfor storing such reports (for example servers or other systems of a“cloud computing” architecture). In one embodiment, a computer-readablemedium includes a medium suitable for transmission of a result of ananalysis of a biological sample.

Datasets and sequence libraries as disclosed herein are consistent withcomputer-based phase assignment of nucleic acid sequence information,such as that which is obtained through the sequencing of a heterozygousdiploid eukaryotic genome. Computers that analyze such data may assignreads into scaffolds, in some cases generating maps that comprise entire‘end-to-end’ chromosome maps for a sample genome. However, mostapproaches are unable to assign heterozygous sequence to a common phasewhen said heterozygous sequence is separated by greater than a readlength of the sequencing technology. Thus, heterozygous loci are notaccurately mapped to a common phase using most computer-based genomeassembly approaches.

Methods, databases and systems disclosed herein allow for the assignmentof heterozygous sequence information to a common phase, even when theheterozygous loci are separated by more than the sequence distancegenerated by a single long read. As such, the methods, databases andsystems disclosed herein provide for the improvement in performance ofcomputer systems related to genome sequencing and genome sequenceassembly. For example, techniques of the present disclosure can allowfor improving the calculation speed, thereby reducing computational timeor computational burden. These techniques can also allow for reducedmemory requirements, including transient memory and non-transient datastorage requirements. In some cases, techniques of the presentdisclosure can enable the computation of previously non-computablecalculations.

The detailed description is further supplemented with reference to thefollowing numbered embodiments. 1. A method of generating long-distancephase information from a first DNA molecule, comprising: a) providing afirst DNA molecule having a first segment and a second segment, whereinthe first segment and the second segment are not adjacent on the firstDNA molecule; b) contacting the first DNA molecule to a DNA bindingmoiety such that the first segment and the second segment are bound tothe DNA binding moiety independent of a common phosphodiester backboneof the first DNA molecule; c) cleaving the first DNA molecule such thatthe first segment and the second segment are not joined by a commonphosphodiester backbone; d) attaching the first segment to the secondsegment via a phosphodiester bond to form a reassembled first DNAmolecule; and e) sequencing at least 4 kb of consecutive sequence of thereassembled first DNA molecule comprising a junction between the firstsegment and the second segment in a single sequencing read, whereinfirst segment sequence and second segment sequence representlong-distance phase information from a first DNA molecule. 2. The methodof numbered embodiment 1, wherein the DNA binding moiety comprises aplurality of DNA-binding molecules. 3. The method of any one of numberedembodiments 1-2, wherein contacting the first DNA molecule to aplurality of DNA-binding molecules comprises contacting to a populationof DNA-binding proteins. 4. The method of any one of numberedembodiments 1-3, wherein the population of DNA-binding proteinscomprises nuclear proteins. 5. The method of any one of numberedembodiments 1-4, wherein the population of DNA-binding proteinscomprises nucleosomes. 6. The method of any one of numbered embodiments1-5, wherein the population of DNA-binding proteins comprises histones.7. The method of any one of numbered embodiments 1-6, wherein contactingthe first DNA molecule to a plurality of DNA-binding moieties comprisescontacting to a population of DNA-binding nanoparticles. 8. The methodof any one of numbered embodiments 1-7, wherein the first DNA moleculehas a third segment not adjacent on the first DNA molecule to the firstsegment or the second segment, wherein the contacting in (b) isconducted such that the third segment is bound to the DNA binding moietyindependent of the common phosphodiester backbone of the first DNAmolecule, wherein the cleaving in (c) is conducted such that the thirdsegment is not joined by a common phosphodiester backbone to the firstsegment and the second segment, wherein the attaching comprisesattaching the third segment to the second segment via a phosphodiesterbond to form the reassembled first DNA molecule, and wherein theconsecutive sequence sequenced in (e) comprises a junction between thesecond segment and the third segment in a single sequencing read. 9. Themethod of any one of numbered embodiments 1-9, comprising contacting thefirst DNA molecule to a cross-linking agent. 10. The method of any oneof any one of numbered embodiments 1-9, comprising contacting the firstDNA molecule to a cross-linking agent. 11. The method of any one ofnumbered embodiments 1-10, wherein the cross-linking agent isformaldehyde. 12. The method of any one of numbered embodiments 1-11,wherein the cross-linking agent is formaldehyde. 13. The method of anyone of numbered embodiments 1-12, wherein the DNA binding moiety isbound to a surface comprising a plurality of DNA binding moieties. 14.The method of any one of numbered embodiments 1-13, wherein the DNAbinding moiety is bound to a solid framework comprising a bead. 15. Themethod of any one of numbered embodiments 1-14, wherein cleaving thefirst DNA molecule comprises contacting to a restriction endonuclease.16. The method of any one of numbered embodiments 1-15, wherein cleavingthe first DNA molecule comprises contacting to a nonspecificendonuclease. 17. The method of any one of numbered embodiments 1-16,wherein cleaving the first DNA molecule comprises contacting to atagmentation enzyme. 18. The method of any one of numbered embodiments1-17, wherein cleaving the first DNA molecule comprises contacting to atransposase. 19. The method of any one of numbered embodiments 1-18,wherein cleaving the first DNA molecule comprises shearing the firstmolecule. 20. The method of any one of numbered embodiments 1-19,comprising adding a tag to at least one exposed end. 21. The method ofany one of numbered embodiments 1-20, wherein the tag comprises alabeled base. 22. The method of any one of numbered embodiments 1-21,wherein the tag comprises a methylated base. 23. The method of any oneof numbered embodiments 1-22, wherein the tag comprises a biotinylatedbase. 24. The method of any one of numbered embodiments 1-23, whereinthe tag comprises uridine. 25. The method of any one of numberedembodiments 1-24, wherein the tag comprises a noncanonical base. 26. Themethod of any one of numbered embodiments 1-25, wherein the taggenerates a blunt ended exposed end. 27. The method of any one ofnumbered embodiments 1-26, comprising adding at least one base to arecessed strand of a first segment sticky end. 28. The method of any oneof any one of numbered embodiments 1-27, comprising adding a linkeroligo comprising an overhang that anneals to the first segment stickyend. 29. The method of any one of any one of numbered embodiments 1-28,wherein the linker oligo comprises an overhang that anneals to the firstsegment sticky end and an overhang that anneals to the second segmentsticky end. 30. The method of any one of any one of numbered embodiments1-29, wherein the linker oligo does not comprise two 5′ phosphatemoieties. 31. The method of any one of numbered embodiments 1-30,wherein attaching comprises ligating. 32. The method of any one ofnumbered embodiments 1-31, wherein attaching comprises DNA single strandnick repair. 33. The method of any one of numbered embodiments 1-32,wherein the first segment and the second segment are separated by atleast 10 kb on the first DNA molecule prior to cleaving the first DNAmolecule. 34. The method of any one of numbered embodiments 1-33,wherein the first segment and the second segment are separated by atleast 15 kb on the first DNA molecule prior to cleaving the first DNAmolecule. 35. The method of any one of numbered embodiments 1-34,wherein the first segment and the second segment are separated by atleast 30 kb on the first DNA molecule prior to cleaving the first DNAmolecule. 36. The method of any one of numbered embodiments 1-35,wherein the first segment and the second segment are separated by atleast 50 kb on the first DNA molecule prior to cleaving the first DNAmolecule. 37. The method of any one of numbered embodiments 1-36,wherein the first segment and the second segment are separated by atleast 100 kb on the first DNA molecule prior to cleaving the first DNAmolecule. 38. The method of any one of numbered embodiments 1-37,wherein the sequencing comprises single molecule long read sequencing.39. The method of any one of numbered embodiments 1-38, wherein the longread sequencing comprises a read of at least 5 kb. 40. The method of anyone of numbered embodiments 1-39, wherein the long read sequencingcomprises a read of at least 10 kb. 41. The method of any one ofnumbered embodiments 140, wherein the first reassembled DNA moleculecomprises a hairpin moiety linking a 5′ end to a 3′ end at one end ofthe first DNA molecule. 42. The method of any one of numberedembodiments 1-42, comprising sequencing a second reassembled version ofthe first DNA molecule. 43. The method of any one of numberedembodiments 1-42, wherein the first segment and the second segment areeach at least 500 bp. 44. The method of any one of numbered embodiments1-43, wherein the first segment, the second segment, and the thirdsegment are each at least 500 bp. 45. A method of genome assemblycomprising: a) obtaining a first DNA molecule complexed to a structure;b) cleaving the first DNA molecule to form a first exposed end and asecond exposed end, wherein the first exposed end and the second exposedend were not adjacent on the molecule prior to said cleaving; c)cleaving the first DNA molecule to form a third exposed end and a fourthexposed end, wherein the third exposed end and the fourth exposed endwere not adjacent on the molecule prior to said cleaving; d) attachingsaid first exposed end and said second exposed end to form a firstjunction; e) attaching said third exposed end and said fourth exposedend to form a second junction f) sequencing across said first junctionand said second junction in a single sequencing read; g) mappingsequence on a first side of said first junction to a first contig ofsaid plurality of contigs; h) mapping sequence on a second side of saidfirst junction to a second contig of said plurality of contigs; i)mapping sequence on a first side of said second junction to a secondcontig of said plurality of contigs; j) mapping sequence on a secondside of said second junction to a third contig of said plurality ofcontigs and k) assigning said first contig, said second contig, and saidthird contig to a common phase of a genome assembly. 46. The method ofnumbered embodiment 45, wherein said plurality of contigs are generatedfrom shotgun sequence data. 47. The method of any one of numberedembodiments 45-46, wherein said plurality of contigs are generated fromsingle molecule long read data. 48. The method of any one of numberedembodiments 45-47, wherein said single molecule long read data comprisessaid plurality of contigs. 49. The method of any one of numberedembodiments 45-48, wherein said plurality of contigs is concurrentlyobtained through sequencing across said first junction and said secondjunction. 50. The method of any one of numbered embodiments 45-49,wherein sequencing across said marker oligo comprises sequencing atleast 10 kb. 51. The method of any one of numbered embodiments 45-50,wherein said structure comprises a population of DNA binding moietiesbound to the first DNA molecule to form reconstituted chromatin. 52. Themethod of any one of numbered embodiments 45-51, wherein saidreconstituted chromatin is contacted to a crosslinking agent. 53. Themethod of any one of numbered embodiments 45-52, wherein saidcrosslinking agent comprises formaldehyde. 54. The method of any one ofnumbered embodiments 45-53, wherein said population of DNA bindingmoieties comprises histones. 55. The method of any one of numberedembodiments 45-54, wherein said population of DNA binding moietiescomprises nanoparticles. 56. The method of any one of numberedembodiments 45-55, wherein said structure comprises native chromatin.57. The method of any one of numbered embodiments 45-56, wherein thefirst exposed end and the second exposed end are separated by at least10 kb on the first DNA molecule prior to cleaving the first DNAmolecule. 58. The method of any one of numbered embodiments 45-57,wherein the first exposed end and the second exposed end are separatedby at least 15 kb on the first DNA molecule prior to cleaving the firstDNA molecule. 59. The method of any one of numbered embodiments 45-58,wherein the first exposed end and the second exposed end are separatedby at least 30 kb on the first DNA molecule prior to cleaving the firstDNA molecule. 60. The method of any one of numbered embodiments 45-59,wherein the first exposed end and the second exposed end are separatedby at least 50 kb on the first DNA molecule prior to cleaving the firstDNA molecule. 61. The method of any one of numbered embodiments 45-60,wherein the first exposed end and the second exposed end are separatedby at least 100 kb on the first DNA molecule prior to cleaving the firstDNA molecule. 62. The method of any one of numbered embodiments 45-61,comprising sequencing a second copy of the first DNA molecule. 63. Arearranged nucleic acid molecule of at least 5 kb comprising a) a firstsegment; b) a second segment; and c) a third segment; d) said firstsegment and said second segment being joined at a first junction; and e)said second segment and said third segment being joined at a secondjunction; wherein said first segment, said second segment and said thirdsegment exist in phase separated by at least 10 kb in an unrearrangednucleic acid molecule, and wherein at least 70% of said rearrangednucleic acid molecule maps to said common unrearranged nucleic acidmolecule. 64. The rearranged nucleic acid of numbered embodiment 63,wherein the first segment, the second segment and the third segmentcomprise separate genomic nucleic acid sequence from a common nucleicacid molecule of a genome. 65. The rearranged nucleic acid of any one ofnumbered embodiments 63-64, wherein the first segment, the secondsegment and the third segment exist in a common molecule in the genomein an order that is rearranged in the rearranged nucleic acid. 66. Therearranged nucleic acid of any one of numbered embodiments 63-65,wherein said nucleic acid molecule is at least 30 kb in length. 67. Therearranged nucleic acid of any one of numbered embodiments 63-66,wherein said nucleic acid comprises a hairpin loop at a double-strandedterminal end, so that the molecule comprises a single strand comprisinga 30 kb inverted repeat. 68. The rearranged nucleic acid of any one ofnumbered embodiments 63-67, wherein said nucleic acid is adouble-stranded circular molecule. 69. The rearranged nucleic acid ofany one of numbered embodiments 63-68, wherein at least 80% of saidrearranged nucleic acid molecule maps to said common unrearrangednucleic acid molecule. 70. The rearranged nucleic acid of any one ofnumbered embodiments 63-69, wherein at least 85% of said rearrangednucleic acid molecule maps to said common unrearranged nucleic acidmolecule. 71. The rearranged nucleic acid of any one of numberedembodiments 63-70, wherein at least 90% of said rearranged nucleic acidmolecule maps to said common unrearranged nucleic acid molecule. 72. Therearranged nucleic acid of any one of numbered embodiments 63-71,wherein at least 95% of said rearranged nucleic acid molecule maps tosaid common unrearranged nucleic acid molecule. 73. The rearrangednucleic acid of any one of numbered embodiments 63-72, wherein at least99% of said rearranged nucleic acid molecule maps to said commonunrearranged nucleic acid molecule. 74. The rearranged nucleic acid ofany one of numbered embodiments 63-73, wherein at least 80% of segmentsof said rearranged nucleic acid molecule maps to said commonunrearranged nucleic acid molecule. 75. The rearranged nucleic acid ofany one of numbered embodiments 63-74, wherein at least 85% of segmentsof said rearranged nucleic acid molecule maps to said commonunrearranged nucleic acid molecule. 76. The rearranged nucleic acid ofany one of numbered embodiments 63-75, wherein at least 90% of segmentsof said rearranged nucleic acid molecule maps to said commonunrearranged nucleic acid molecule. 77. The rearranged nucleic acid ofany one of numbered embodiments 63-76, wherein at least 95% of segmentsof said rearranged nucleic acid molecule maps to said commonunrearranged nucleic acid molecule. 78. The rearranged nucleic acid ofany one of numbered embodiments 63-77, wherein at least 99% of segmentsof said rearranged nucleic acid molecule maps to said commonunrearranged nucleic acid molecule. 79. The rearranged nucleic acid ofany one of numbered embodiments 63-78, wherein the rearranged nucleicacid is generated by steps of the method of any one or more of numberedembodiments 1-62. 80. A method of generating a phased sequence of asample nucleic acid molecule comprising a) generating a first rearrangednucleic acid molecule of any one of numbered embodiments 63-78 from thesample nucleic acid molecule; b) generating a second rearranged nucleicacid molecule of any one of numbered embodiments 63-78 from the samplenucleic acid molecule; and c) sequencing the first rearranged nucleicacid molecule and the second rearranged nucleic acid molecule; whereinthe first rearranged nucleic acid molecule and the second rearrangednucleic acid molecule are independently generated 81. A method ofgenerating a phased sequence of a sample nucleic acid moleculecomprising a) sequencing a first rearranged nucleic acid molecule of anyone of numbered embodiments 63-78 from the sample nucleic acid molecule;b) sequencing a second rearranged nucleic acid molecule of any one ofnumbered embodiments 63-78 from the sample nucleic acid molecule;wherein the first rearranged nucleic acid molecule and the secondrearranged nucleic acid molecule are independently generated; and c)assembling sequence of the first rearranged nucleic acid molecule of anyone of numbered embodiments 63-78 and the second rearranged nucleic acidmolecule of any one of numbered embodiments 63-78 such that an assembledsequence is an unrearranged phased sequence of a sample nucleic acidmolecule. 82. The method of any one of numbered embodiments 80-81,wherein sequencing a first rearranged nucleic acid molecule comprisesgenerating a sequence read of at least 1 kb. 83. The method of any oneof numbered embodiments 80-82, wherein sequencing a first rearrangednucleic acid molecule comprises generating a sequence read of at least 2kb. 84. The method of any one of numbered embodiments 80-83, whereinsequencing a first rearranged nucleic acid molecule comprises generatinga sequence read of at least 5 kb. 85. The method of any one of numberedembodiments 80-84, comprising assigning at least 70% of said firstrearranged molecule to a common phase of a single genomic molecule. 86.The method of any one of numbered embodiments 80-85, comprisingassigning at least 70% of said second rearranged molecule to a commonphase of a single genomic molecule. 87. The method of any one ofnumbered embodiments 80-86, comprising assigning at least 80% of saidfirst rearranged molecule to a common phase of a single genomicmolecule. 88. The method of any one of numbered embodiments 80-87,comprising assigning at least 80% of said second rearranged molecule toa common phase of a single genomic molecule. 89. The method of any oneof numbered embodiments 80-88, comprising assigning at least 90% of saidfirst rearranged molecule to a common phase of a single genomicmolecule. 90. The method of any one of numbered embodiments 80-89,comprising assigning at least 90% of said second rearranged molecule toa common phase of a single genomic molecule. 91. The method of any oneof numbered embodiments 80-90, comprising assigning at least 95% of saidfirst rearranged molecule to a common phase of a single genomicmolecule. 92. The method of any one of numbered embodiments 80-91,comprising assigning at least 95% of said second rearranged molecule toa common phase of a single genomic molecule. 93. A method of phasinglong-read sequence data comprising a) obtaining sequence data from thenucleic acid sample of any one of numbered embodiments 63-78; b)obtaining long-read sequence data from the rearranged nucleic acid ofany one of numbered embodiments 63-78; c) mapping the long-read sequencedata from the rearranged nucleic acid of any one of numbered embodiments63-78 to the sequence data from the nucleic acid sample; and d)assigning to a common phase the sequence data from the nucleic acidsample mapped to by the long-read sequence data from the rearrangednucleic acid of any one of numbered embodiments 63-78. 94. A method ofproviding phase information to a nucleic acid dataset generated from anucleic acid sample by a DNA sequencing technology, comprising a)obtaining a nucleic acid of said nucleic acid sample having a firstsegment and a second segment separated by a distance greater than a readlength of the DNA sequencing technology b) shuffling the nucleic acidsuch that the first segment and the second segment are separated by adistance less than a read length of the DNA sequencing technology; c)sequencing the shuffled nucleic acid using the DNA sequencing technologysuch that the first segment and the second segment appear in a singleread of the DNA sequencing technology; and d) assigning sequence readsof the data set comprising first segment sequence and sequence reads ofthe data set comprising second segment sequence to a common phase. 95.The method of numbered embodiment 94, wherein the DNA sequencingtechnology generates reads having a read length of at least 10 kb. 96.The method of any one of numbered embodiments 94-94, wherein shufflingcomprises performing steps of any one of any one of numbered embodiments1-62. 97. The method of any one of numbered embodiments 94-94, whereinthe first segment and the second segment are separated by a linker oligothat marks a segment end. 98. A nucleic acid sequence databasecomprising sequence information obtained from a plurality of moleculesof any one of numbered embodiments 63-78, wherein sequence informationcorresponding to molecules having less than 70% of their segments map toa common scaffold is excluded from at least one analysis. 99. A nucleicacid sequence database comprising sequence information obtained from aplurality of molecules of any one of numbered embodiments 63-78, whereinsequence information corresponding to molecules having less than 70% oftheir sequence information map to a common scaffold is excluded from atleast one analysis. 100. A method of phasing long-read sequence datacomprising a) obtaining sequence data from the nucleic acid sample ofany one of numbered embodiments 63-78; b) obtaining long-read sequencedata from the rearranged nucleic acid of the rearranged nucleic acid ofany one of numbered embodiments 63-78; c) mapping the first segment, thesecond segment and the third segment of the rearranged nucleic acid ofany one of numbered embodiments 63-78 to the sequence data from thenucleic acid sample to the nucleic acid sample sequence data; and d)when at least two segments map to a common scaffold, assigning sequencevariation of said segments to a common phase. 101. The method ofnumbered embodiment 100, wherein the first segment comprises a singlenucleotide polymorphism relative to the sequence data from the nucleicacid sample. 102. The method of any one of numbered embodiments 100-101,wherein the first segment comprises an insertion relative to thesequence data from the nucleic acid sample. 103. The method of any oneof numbered embodiments 100-102, wherein the first segment comprises adeletion relative to the sequence data from the nucleic acid sample.104. The method of any one of numbered embodiments 100-103, comprisingassigning a first set of segments mapping to a first common scaffold toa common phase of the first common scaffold, and assigning a second setof segments mapping to a second common scaffold to a common phase of thesecond common scaffold. 105. A nucleic acid sequence library of anucleic acid sample, said nucleic acid sequence library comprising apopulation of nucleic acid sequence reads having an average read length,at least one of said reads comprising at least 500 bases of a firstnucleic acid segment and at least 500 bases of a second nucleic acidsegment, wherein said first nucleic acid segment and said second nucleicacid segment are found in phase separated by a distance greater thansaid average read length on a common molecule of said nucleic acidsample. 106. The nucleic acid sequence library of numbered embodiment105, wherein said first nucleic acid segment and said second nucleicacid segment are found in phase separated by a distance greater than 10kb. 107. The nucleic acid sequence library of any one of numberedembodiments 105-106, wherein said first nucleic acid segment and saidsecond nucleic acid segment are found in phase separated by a distancegreater than 20 kb. 108. The nucleic acid sequence library of any one ofnumbered embodiments 105-107, wherein said first nucleic acid segmentand said second nucleic acid segment are found in phase separated by adistance greater than 50 kb. 109. The nucleic acid sequence library ofany one of numbered embodiments 105-108, wherein said first nucleic acidsegment and said second nucleic acid segment are found in phaseseparated by a distance greater than 100 kb. 110. The nucleic acidsequence library of any one of numbered embodiments 105-109, wherein atleast one of said reads comprises at least 1 kb of a first nucleic acidsegment. 111. The nucleic acid sequence library of any one of numberedembodiments 105-110, wherein at least one of said reads comprises atleast 5 kb of a first nucleic acid segment. 112. The nucleic acidsequence library of any one of numbered embodiments 105-111, wherein atleast one of said reads comprises at least 10 kb of a first nucleic acidsegment. 113. The nucleic acid sequence library of any one of numberedembodiments 105-112, wherein at least one of said reads comprises atleast 20 kb of a first nucleic acid segment. 114. The nucleic acidsequence library of any one of numbered embodiments 105-113, wherein atleast one of said reads comprises at least 50 kb of a first nucleic acidsegment. 115. The nucleic acid sequence library of any one of numberedembodiments 105-114, wherein nucleic acid sequence library comprises atleast 80% of said nucleic acid sample. 116. The nucleic acid sequencelibrary of any one of numbered embodiments 105-115, wherein nucleic acidsequence library comprises at least 85% of said nucleic acid sample.117. The nucleic acid sequence library of any one of numberedembodiments 105-116, wherein nucleic acid sequence library comprises atleast 90% of said nucleic acid sample. 118. The nucleic acid sequencelibrary of any one of numbered embodiments 105-117, wherein nucleic acidsequence library comprises at least 95% of said nucleic acid sample.119. The nucleic acid sequence library of any one of numberedembodiments 105-118, wherein nucleic acid sequence library comprises atleast 99% of said nucleic acid sample. 120. The nucleic acid sequencelibrary of any one of numbered embodiments 105-119, wherein nucleic acidsequence library comprises at least 99.9% of said nucleic acid sample.121. A nucleic acid sequence library of a nucleic acid sample, saidnucleic acid sequence library comprising a population of nucleic acidsequence reads having a mean length of at least 1 kb, said readsindependently comprising at least 300 bases of sequence from twoseparate in phase regions of the nucleic acid sample, said two separatein phase regions separated by a distance greater than 10 kb in thenucleic acid sample. 122. The nucleic acid sequence library of numberedembodiment 121, wherein said reads independently comprise at least 500bases of sequence from two separate in phase regions of the nucleic acidsample. 123. The nucleic acid sequence library of any one of numberedembodiments 121-122, wherein said reads independently comprise at least1 kb of sequence from two separate in phase regions of the nucleic acidsample. 124. The nucleic acid sequence library of any one of numberedembodiments 121-123, wherein said reads independently comprise at least2 kb of sequence from two separate in phase regions of the nucleic acidsample. 125. The nucleic acid sequence library of any one of numberedembodiments 121-124, wherein said reads independently comprise at least5 kb of sequence from two separate in phase regions of the nucleic acidsample. 126. The nucleic acid sequence library of any one of numberedembodiments 121-125, wherein said reads independently comprise at least10 kb of sequence from two separate in phase regions of the nucleic acidsample. 127. The nucleic acid sequence library of any one of numberedembodiments 121-126, wherein said two separate in phase regions areseparated by a distance greater than 20 kb in the nucleic acid sample.128. The nucleic acid sequence library of any one of numberedembodiments 121-127, wherein said two separate in phase regions areseparated by a distance greater than 30 kb in the nucleic acid sample.129. The nucleic acid sequence library of any one of numberedembodiments 121-128, wherein said two separate in phase regions areseparated by a distance greater than 50 kb in the nucleic acid sample inat least 1% of the reads. 130. The nucleic acid sequence library of anyone of numbered embodiments 121-129, wherein said two separate in phaseregions are separated by a distance greater than 100 kb in the nucleicacid sample in at least 1% of the reads. 131. The nucleic acid sequencelibrary of any one of numbered embodiments 121-130, wherein nucleic acidsequence library comprises at least 80% of said nucleic acid sample.132. The nucleic acid sequence library of any one of numberedembodiments 121-131, wherein nucleic acid sequence library comprises atleast 85% of said nucleic acid sample. 133. The nucleic acid sequencelibrary of any one of numbered embodiments 121-132, wherein nucleic acidsequence library comprises at least 90% of said nucleic acid sample.134. The nucleic acid sequence library of any one of numberedembodiments 121-133, wherein nucleic acid sequence library comprises atleast 95% of said nucleic acid sample. 135. The nucleic acid sequencelibrary of any one of numbered embodiments 121-134, wherein nucleic acidsequence library comprises at least 99% of said nucleic acid sample.136. The nucleic acid sequence library of any one of numberedembodiments 121-135, wherein nucleic acid sequence library comprises atleast 99.9% of said nucleic acid sample. 137. A nucleic acid librarygenerated from a nucleic acid sample, wherein at least 80% of nucleicacid sequence of the nucleic acid sample is represented in the nucleicacid library; and in phase sequence segments of the nucleic acid sampleare rearranged such that at least one distantly positioned pair of inphase segments of the nucleic acid sample is read in a single sequenceread; such that sequencing said library concurrently generates contiginformation spanning at least 80% of the nucleic acid sample, and phaseinformation sufficient to order and orient said contig information togenerate a phased sequence of said nucleic acid sample. 138. The nucleicacid library of numbered embodiment 137, wherein at least 90% of nucleicacid sequence of the nucleic acid sample is represented in the nucleicacid library. 139. The nucleic acid library of any one of numberedembodiments 137-138, wherein at least 95% of nucleic acid sequence ofthe nucleic acid sample is represented in the nucleic acid library. 140.The nucleic acid library of any one of numbered embodiments 137-139,wherein at least 99% of nucleic acid sequence of the nucleic acid sampleis represented in the nucleic acid library. 141. The nucleic acidlibrary of any one of numbered embodiments 137-140, wherein said 80% ofnucleic acid sequence of the nucleic acid sample is obtained from nomore than 100,000 library constituents. 142. The nucleic acid library ofany one of numbered embodiments 137-141, wherein said 80% of nucleicacid sequence of the nucleic acid sample is obtained from no more than10,000 library constituents. 143. The nucleic acid library of any one ofnumbered embodiments 137-142, wherein said 80% of nucleic acid sequenceof the nucleic acid sample is obtained from no more than 1,000 libraryconstituents. 144. The nucleic acid library of any one of numberedembodiments 137-143, wherein said 80% of nucleic acid sequence of thenucleic acid sample is obtained from no more than 500 libraryconstituents. 145. The nucleic acid library of any one of any one ofnumbered embodiments 137-144, wherein the sample is a genomic sample.146. The nucleic acid library of any one of any one of numberedembodiments 137-145, wherein the sample is a eukaryotic genomic sample.147. The nucleic acid library of any one of any one of numberedembodiments 137-146, wherein the sample is a plant genomic sample. 148.The nucleic acid library of any one of any one of numbered embodiments137-147, wherein the sample is an animal genomic sample. 149. Thenucleic acid library of any one of any one of numbered embodiments137-148, wherein the sample is a mammalian genomic sample. 150. Thenucleic acid library of any one of any one of numbered embodiments137-149, wherein the sample is a unicellular eukaryotic genomic sample.151. The nucleic acid library of any one of any one of numberedembodiments 137-150, wherein the sample is a human genomic sample. 152.The nucleic acid library of any one of numbered embodiments 137-151,wherein the nucleic acid library is not barcoded to preserve phaseinformation. 153. The nucleic acid library of any one of numberedembodiments 137-152, wherein a read of said library comprises at least 1kb of sequence from a first region and at least 100 bases of sequencefrom a second region in phase the first region and separated by greaterthan 50 kb from the first region in the sample. 154. A method ofconfiguring a nucleic acid molecule for sequencing on a sequencingdevice, wherein the nucleic acid molecule comprises at least 100 kb ofsequence, and wherein said at least 100 kb of sequence comprises a firstsegment and a second segment separated by a length greater than a readlength of the sequencing device, comprising changing a relative positionof the first segment relative to the second segment of the nucleic acidmolecule, such that the first segment and the segment are separated byless than the read length of the sequencing device; wherein phaseinformation for the first segment and the second segment is maintained;and wherein no more than 10% of the nucleic acid molecule is deleted.155. The method of numbered embodiment 154, comprising generating a readspanning at least part of the first segment and the second segment. 156.The method of any one of numbered embodiments 154-155, comprisingassigning the first segment and the second segment to a common phase ofa sequence of the nucleic acid molecule. 157. The method of any one ofnumbered embodiments 154-156, wherein no more than 5% of the nucleicacid molecule is deleted. 158. The method of any one of numberedembodiments 154-157, wherein no more than 1% of the nucleic acidmolecule is deleted. 159. The method of any one of numbered embodiments154-158, wherein the first segment and the second segment are separatedby at least 10 kb in the nucleic acid molecule prior to configuring.160. The method of any one of numbered embodiments 154-159, wherein thefirst segment and the second segment are separated by at least 50 kb inthe nucleic acid molecule prior to configuring. 161. The method of anyone of numbered embodiments 154-160, wherein the first segment and thesecond segment are separated by a junction marker following saidconfiguring. 162. The method of any one of numbered embodiments 154-161,comprising attaching a stem loop at an end of the nucleic acid, therebyconverting the molecule to a single strand. 163. The method of any oneof numbered embodiments 154-162, comprising circularizing the nucleicacid molecule. 164. The method of any one of numbered embodiments154-163, comprising attaching the nucleic acid molecule to a DNApolymerase. 165. The method of any one of numbered embodiments 154-164,comprising binding the nucleic acid molecule such that the first segmentand the second segment are held together independent of a phosphodiesterbackbone; cleaving a phosphodiester backbone between the first segmentand the second segment at at least two positions; and reattaching thefirst segment to the second segment, such that the first segment and thesecond segment are separated by less than a read length of thesequencing device. 166. The method of any one of numbered embodiments154-165, wherein said cleaving and said reattaching does not result inloss of sequence information form said nucleic acid molecule. 167. Amethod of generating long-distance phase information from a firstnucleic acid molecule, comprising: a) providing a sample comprising afirst nucleic acid molecule having a first segment, a second segment,and a third segment, wherein none of the first segment, the secondsegment, and the third segment are adjacent on the first nucleic acidmolecule, wherein the first nucleic acid molecule is contacted to aframework such that the first segment, the second segment, and the thirdsegment are bound to the framework independent of a commonphosphodiester backbone of the first nucleic acid molecule; b) cleavingthe first nucleic acid molecule such that the first segment, the secondsegment, and the third segment are not joined by a common phosphodiesterbackbone; c) connecting the first segment to the second segment andconnecting the second segment to the third segment; and d) sequencing afirst portion of the first nucleic acid molecule comprising the firstsegment, the second segment, and the third segment, thereby generatingfirst segment sequence information, second segment sequence information,and third segment sequence information, wherein the first segmentsequence information, the second segment sequence information, and thethird segment sequence information provide long-distance phaseinformation about the first nucleic acid molecule. 168. The method ofnumbered embodiment 167, wherein the framework comprises reconstitutedchromatin. 169. The method of any one of numbered embodiments 167-168,wherein the framework comprises native chromatin. 170. The method of anyone of numbered embodiments 167-169, wherein the cleaving is conductedwith a restriction enzyme. 171. The method of any one of numberedembodiments 167-170, wherein the cleaving is conducted with fragmentase.172. The method of any one of numbered embodiments 167-171, furthercomprising, prior to the sequencing, removing from the sample a secondportion of the first nucleic acid molecule comprising at most twosegments. 173. The method of any one of numbered embodiments 167-172,further comprising assembling a sequence of the first nucleic acidmolecule using the first segment sequence information, the secondsegment sequence information, and the third segment sequenceinformation. 174. A method of sequencing a nucleic acid molecule,comprising: obtaining a first nucleic acid molecule comprising a firstsegment, a second segment and a third segment sharing a commonphosphodiester backbone, wherein none of said first segment, secondsegment and third segment are adjacent on said first nucleic acidmolecule; partitioning said nucleic acid molecule such that said firstsegment, second segment and third segment are associated independent oftheir common phosphodiester backbone; cleaving said nucleic acidmolecule to generate fragments such that there is no continuousphosphodiester backbone linking the first segment, second segment andthird segment; ligating said fragments such that said first segment,second segment and third segment are consecutive on a rearranged nucleicacid molecule sharing a common phosphodiester backbone; and sequencingat least a portion of said rearranged nucleic acid molecule such that atleast 5,000 bases of said rearranged nucleic acid molecule are sequencedin a single read. 175. The method of numbered embodiment 174, whereinpartitioning comprises contacting said nucleic acid molecule to abinding moiety such that said first segment, second segment and thirdsegment are bound in a common complex independent of their commonphosphodiester backbone. 176. The method of any one of numberedembodiments 174-175, wherein contacting the nucleic acid molecule to aplurality of DNA-binding molecules comprises contacting to a populationof DNA-binding proteins. 177. The method of any one of numberedembodiments 174-176, wherein the population of DNA-binding proteinscomprises nuclear proteins. 178. The method of any one of numberedembodiments 174-177, wherein the population of DNA-binding proteinscomprises nucleosomes. 179. The method of any one of numberedembodiments 174-178, wherein the population of DNA-binding proteinscomprises histones. 180. The method of any one of numbered embodiments174-179, wherein contacting the nucleic acid molecule to a plurality ofDNA-binding moieties comprises contacting to a population of DNA-bindingnanoparticles. 181. The method of any one of numbered embodiments174-180, wherein cleaving the nucleic acid molecule comprises contactingto a restriction endonuclease. 182. The method of any one of numberedembodiments 174-181, wherein cleaving the nucleic acid moleculecomprises contacting to a nonspecific endonuclease. 183. The method ofany one of numbered embodiments 174-182, wherein cleaving the nucleicacid molecule comprises contacting to a tagmentation enzyme. 184. Themethod of any one of numbered embodiments 174-183, wherein cleaving thenucleic acid molecule comprises contacting to a transposase. 185. Themethod of any one of numbered embodiments 174-184, wherein cleaving thenucleic acid molecule comprises shearing the first molecule. 186. Themethod of any one of numbered embodiments 174-185, wherein partitioningcomprises separating said nucleic acid molecule from other nucleic acidmolecules of a sample. 187. The method of any one of numberedembodiments 174-186, wherein partitioning comprises diluting saidnucleic acid sample. 188. The method of any one of numbered embodiments174-187, wherein partitioning comprises distributing said nucleic acidmolecule into a microdroplet of an emulsion. 189. A nucleic acidmolecule representative of genomic phase information of an organisms'sgenome, said nucleic acid molecule comprising at least 20 kb of nucleicacid sequence information that maps to a single genomic molecule,wherein said sequence information comprises segments rearranged relativeto their position in the genomic molecule, and wherein at least 70% ofsequence information that uniquely maps to said organism's genome mapsto a single genomic molecule. 190. The nucleic acid molecule of numberedembodiment 189, wherein the nucleic acid molecule comprises at least 20segments. 191. The nucleic acid molecule of any one of numberedembodiments 189-190, wherein said segments are not adjacent in saidorganism's genome. 192. A nucleic acid library comprising at least 100nucleic acid molecule constituents of at least 20 kb, whereinconstituents comprise rearranged segments of an organism's genome;wherein at least 70% of uniquely mapping segments from a libraryconstituent map to a common genomic molecule; and wherein constituentsare not bound to nucleic acid binding moieties. 193. A nucleic aciddataset comprising sequences corresponding to at least 100 nucleic acidmolecule constituents of at least 20 kb, wherein constituents compriseat least 5 rearranged segments of an organism's genome, and whereinconstituents for which less than 70% of said rearranged segments map toa common scaffold are excluded from a downstream analysis. 194. Anucleic acid dataset comprising sequences corresponding to at least 100nucleic acid molecule constituents of at least 20 kb, whereinconstituents comprise at least 5 rearranged segments of an organism'sgenome, and wherein constituents for which less than 70% of saidsequence uniquely maps to a common scaffold are excluded from adownstream analysis.

Referring to the Figures, one sees illustration of certain embodimentsdiscussed herein. At FIG. 1, one sees an intermediate in the process ofconstructing a punctuated, rearranged phase-preserving nucleic acidmolecule. A single nucleic acid molecule has been bound to a nucleicacid binding moiety, such as a reconstituted chromatin complex, andcontacted to formaldehyde to crosslink the complex. The complex involvesa single nucleic acid starting molecule, which forms a cluster with thenucleic acid-binding components, collectively referred to asreconstituted chromatin, such that only internal loops of the nucleicacid molecule protrude from the cluster. The protruding loops arecleaved using the restriction endonuclease MboI to generate sticky ends,as depicted in FIG. 1.

In alternate embodiments, the nucleic acid molecule is bound to a beador surface, such as a SPRI coated or other nucleic acid-binding agentcoated bead. The nucleic acid sample is bound under conditions such thatonly one nucleic acid molecule is bound per bead, or such that boundnucleic acids are unlikely to cross-ligate after cleavage. Also,cleavage is alternately accomplished using another restrictionendonuclease, a transposase, a tagmentation enzyme, a nonspecificendonuclease, a topoisomerase or other agent having endonucleaseactivity.

At FIG. 2, one sees that the cleaved nucleic acid complex of FIG. 1 istreated using a nucleic acid polymerase and a single population of dGTPso as to fill in a single position of the overhang. The fill-in stepprevents sticky ends of the complex from cross-annealing and ligating ina later step. In some cases, the step is excluded, and complexes areallowed to cross-ligate without punctuation oligos. Alternately, bluntends are generated, or tagmentation adapters are added though the actionof a transposase rather than a restriction endonuclease.

FIG. 3 shows the complex of FIG. 1 and FIG. 2 following annealing andligation of punctuation oligos to the exposed ends of the complex.Punctuation oligos are depicted as thin solid lines rather than asnucleic acid base sequence. Punctuation oligos are optionally modifiedso as to preclude concatemerization, for example by removal of 5′phosphate groups. Punctuation oligos are optionally designed to becompatible with the free sticky ends as modified in FIG. 2. In otherembodiments, cleaved nucleic acid ends can be ligated to each otherdirectly, without intervening punctuation oligos.

FIG. 4 depicts the released punctuated nucleic acid molecule followingreversal of crosslinking and liberation from the reconstituted chromatinthrough treatment using proteinase K. The end-product punctuated nucleicacid comprises segments 400 separated by punctuation oligos 401. Thesegments preserve the phase information of the original nucleic acidmolecule but are randomly ordered and oriented relative to the beginningmolecule. Substantially all of the sequence of the original nucleic acidmolecule is present in the punctuated molecule, such that sequencing thepunctuated molecule generates sequence information sufficient togenerate de novo contigs.

Upon sequencing the punctuated nucleic acid using a long-read sequencingdevice, one observes stretches of sequence that correspond to uncleavedsegments, for which local order and orientation, as well as phaseinformation is derived. One also observes regions of long sequence readsthat span punctuation oligo sequence. These sequence segments on eitherside of a punctuation oligo are known to be in phase with one another(and in phase with other segments on the punctuated molecule), but areunlikely to be in the correct order and orientation. A benefit of therearrangement process is that segments far apart from one another on thesample molecule are brought into proximity such that they are spanned ina single read. Another benefit is that the sequence information of theoriginal sample molecule is largely preserved, such that de novo contiginformation is concurrently generated.

FIG. 5 shows an alternative embodiment of the present disclosure. Aseries of short paired ends 500, each indicative that the sequencesjoined in the pair are in phase, are adapter tagged (e.g., withamplification adapters) 501 and ligated to form a concatenated pairedend multimer 502. Individual pairs, or contigs to which they uniquelymap, are confidently assigned to a common phase. Read pair units oneither side of amplification adapters are not inferred to have an order,orientation, or phase relationship with one another unless additionalmeasures are taken in concatemer assembly.

A benefit of the concatenated molecule of FIG. 5 is that multiple pairedend reads are assembled into a single molecule that is sequenced in asingle or a smaller number of long read reactions, rather than in a muchgreater number of short-run reads. However, because the segment lengthof individual paired ends is shorter, the overall sequence of thestaring sample is unlikely to be preserved in the concatenated molecule,complicating de novo sequencing.

FIG. 6 shows an alternative scenario, whereby a punctuated nucleic acidmolecule 600 is used to generate templates for short-read sequencing.Punctuated nucleic acid molecules are contacted to a population ofprimers 601 that anneal to the punctuation sequence and that comprisebin-specific oligonucleotide barcodes 602. The primers can then beextended, for example, to incorporate sequence 603 complementary to thepunctuated nucleic acid molecule. Through this approach, phaseinformation is derived from the barcode information. A benefit is thatshort-read sequencing is facilitated.

FIG. 7 shows a gel electrophoresis analysis of two samples, before aligation step (‘BF’) and after a ligation step (‘AF’). The left-mostlane contains a DNA ladder, with sizes from top to bottom of 48500,15000, 7000, 4000, 3000, 2500, 2000, 1500, 1200, 900, 600, 400, 250, and100 bp. The second and third lanes from the left contain sample 1 beforeand after ligation, respectively. The fourth and fifth lanes from theleft contain sample 2 before and after ligation, respectively. Both thesample 1 and sample 2 ligated lanes show dark bands of DNA in the7000-48500 bp range, much larger than the bands in either of thepre-ligation lanes. Sample 1 comprises about 7 nanograms DNA permicroliter (ng/μL) with a total of about 200 ng DNA, and sample 2comprises about 115 ng/μL of DNA, with a total of about 3.4 μg DNA.

FIG. 8 presents representative information about the sequencinginformation for a sample. Over 1,000,000 circular consensus sequence(CSS) reads are generated, with 300,000 unmapped reads (25%). There are1,500,000 mapped segments (−q 1) and 1,350,000 mapped segments (−q 20).For reads with 1 mapped segment, n=500,000; for reads with 2 mappedsegments, n=175,000; for reads with 3 mapped segments, n=75,000; forreads with 4 mapped segments, n=30,000; for reads for 5 mapped segments,n=15,000; for reads with 6 mapped segments, n=7,000. Table 1 shows clonecoverage from reads with X maximum number of mapping segments.

FIG. 9A and FIG. 9B show frequency distributions of distance spanned byreads with X mapped segments for a sample, with 10 kb bins (FIG. 9A) and1 kb bins (FIG. 9B). The y axis shows the number of PacBio CCS reads(axis lines from bottom to top: 1, 10, 100, 1000, 10000). The x axisshows the distance spanned by the reads (axis lines from left to right:FIG. 9A: 0, 200000, 400000, 600000, 800000, 1000000; FIG. 9B: 0, 20000,40000, 60000, 80000, 100000). Frequency distributions are shown forreads with 1 mapped segment (901, 911), 2 mapped segments (902, 912), 3mapped segments (903, 913), 4 mapped segments (904, 914), and 5 mappedsegments (905, 915).

FIG. 10 depicts an exemplary computer system 1000 adapted to implement amethod described herein. The system 1000 includes a central computerserver 1001 that is programmed to implement exemplary methods describedherein. The server 1001 includes a central processing unit (CPU, also“processor”) 1005 which can be a single core processor, a multi coreprocessor, or plurality of processors for parallel processing. Theserver 1001 also includes memory 1010 (for example random access memory,read-only memory, flash memory); electronic storage unit 1015 (forexample hard disk); communications interface 1020 (for example networkadaptor) for communicating with one or more other systems; andperipheral devices 1025 which may include cache, other memory, datastorage, and/or electronic display adaptors. The memory 1010, storageunit 1015, interface 1020, and peripheral devices 1025 are incommunication with the processor 1005 through a communications bus(solid lines), such as a motherboard. The storage unit 1015 can be adata storage unit for storing data. The server 1001 is operativelycoupled to a computer network (“network”) 1030 with the aid of thecommunications interface 1020. The network 1030 can be the Internet, anintranet and/or an extranet, an intranet and/or extranet that is incommunication with the Internet, a telecommunication or data network.The network 1030 in some cases, with the aid of the server 1001, canimplement a peer-to-peer network, which may enable devices coupled tothe server 1001 to behave as a client or a server.

The storage unit 1015 can store files, such as subject reports, and/orcommunications with the caregiver, sequencing data, data aboutindividuals, or any aspect of data associated with the invention.

The server can communicate with one or more remote computer systemsthrough the network 1030. The one or more remote computer systems maybe, for example, personal computers, laptops, tablets, telephones, Smartphones, or personal digital assistants.

In some situations, the system 1000 includes a single server 1001. Inother situations, the system includes multiple servers in communicationwith one another through an intranet, extranet and/or the Internet.

The server 1001 can be adapted to store measurement data, patientinformation from the subject, such as, for example, polymorphisms,mutations, medical history, family history, demographic data and/orother information of potential relevance. Such information can be storedon the storage unit 1015 or the server 1001 and such data can betransmitted through a network.

As used herein, nucleic acid segments are ‘in proximity’ when they arein phase and can be included, at least in part, in a single read.

EXAMPLES Example 1. Some Long-Read Sequencing Approaches are Unable toPhase Some Mutations in a Diploid DNA Sample

Treatment of a particular human disease depends on the presence of afunctional gene product. In the presence of this gene product, atherapeutic molecule is metabolized to yield an effective metabolite. Inthe absence of the gene product, the therapeutic molecule accumulatesand is harmful to the patient.

A patient genome is shotgun sequenced, and it is determined that twopoint mutations map to the locus encoding the gene product necessary fortreatment efficacy. The two point mutations are separated by 30 kb inthe assembled shotgun scaffold. Phase information for the two pointmutations is unavailable, so practitioners are unable to determinewhether the patient harbors a wild-type allele and a double-mutantallele, or in the alternative whether the patient independently harborstwo single-mutant null alleles, one at the 5′ end of the locus and asecond at the 3′ end of the locus.

DNA is extracted from a patient and the sample is sequenced on along-read sequencing machine. The limit of a single long read on averageis 10-15 kb. The reads confirm that the patient is heterozygous for boththe first and the second mutation. However, given that the mutations inthe patient's genome are separated by 30 kb, phase information cannot beacquired using the generated sequence information. As a consequence,practitioners are unable to determine whether the patient harbors awild-type allele and a doubly-mutant null allele, and is thereforeeligible for treatment using the therapeutic molecule, or whether thepatient harbors two single mutant null alleles and is therefore unableto metabolize the therapeutic molecule. The patient is denied thetreatment and continues to suffer from the condition.

This example demonstrates that long range sequencing approaches used incombination with shotgun reads do not accurately phase mutations,particularly when the mutations are separated by long stretches ofhomozygous DNA. Furthermore, this example illustrates that failure toaccurately assign phase information to genomic sequence has consequencesfor patient health.

Example 2. Successful Phasing of Mutations in Diploid DNA Sample

DNA from the patient of Example 1 is subjected to phase-analysis usingthe approaches disclosed herein.

DNA is extracted from the patient described in Example 1. A library ofpunctuated, insertion shuffled molecules is generated such that phaseinformation is preserved while the relative positions of sequencesegments are rearranged.

The extracted DNA is assembled in vitro into reconstituted chromatin.The reconstituted chromatin is cleaved with the restriction enzyme MboI.The resulting sticky ends are partially filled in with a single base inorder to prevent re-ligation of the restriction enzyme-generatedoverhangs. Punctuation oligonucleotides, which have 5′ and 3′ endscompatible with the partially filled in overhangs of the digested DNAsample, are added to the DNA sample along with a DNA ligase. Thepunctuation oligonucleotides lack 5′ phosphate groups to avoidconcatemerization of the oligonucleotides. This ligation step results inthe reorganization of DNA segments as ends originally not adjacent toone another are adjacent to each other following ligation. Phaseinformation is maintained since the DNA molecule is bound to crosslinkedreconstituted chromatin scaffolds during this process.

Sufficient sequence information is determined such that complete genomeinformation is obtained without the use of a shotgun sequence stepindependent of phase determination. It is determined that the patient isheterozygous for a first and a second null mutation in the gene ofinterest.

Furthermore, library molecules are observed wherein the first and secondDNA segments containing the two mutations are rearranged without loss ofphase information, such that less than 15 kb of sequence separates them.A read spanning the rearranged region is generated, and is found tocomprise a first and a second null mutation. Since the first and secondDNA segments in the rearranged DNA sample are less than 15 kb apart, thetwo mutations are able to be both be detected in a single sequencingread, leading to phasing information. This phasing information is usedto determine that the patient harbors a double mutant allele. A secondread is observed, having a different junction point, but also having afirst and a second segment spanning the first and the secondheterozygous regions of the locus. It is observed that the first regionand the second region in the rearranged molecule both encode wild-typesequence.

Additional molecules comprising phase-preserving rearrangements aresequenced. The additional molecules are found to have punctuationinserts at different positions relative to one another. None of therearranged molecules harbor a single null mutation and a singlewild-type allele. Instead, all of the sequence reads that span bothheterozygous regions comprise either wild type alleles at both loci, ornull mutations at both loci.

It is determined that the patient genome comprises a double-mutant nullallele and a wild-type allele. It is concluded that the treatment islikely to be effective. The patient is administered the therapeuticmolecule, and the patient's condition is alleviated through thebeneficial activity of the therapeutic molecule.

This example illustrates that the methods and compositions disclosedherein allow concurrent de novo sequence generation and phasing from asingle template library. Separate shotgun sequencing libraries andphase-determination libraries are not required, thus substantiallyreducing cost of the sequencing determination.

This example also illustrates that the methods and compositionsdisclosed herein allow one to accurately, redundantly phase moleculeseven though the molecules are largely identical, and the heterozygouspositions are separated by regions of identity that are greater thantwice the length of the reads in the sequencing technology used.

Example 3. Some Long-Read Sequencing Approaches are Unsuccessful inPhasing of Transposon-Rich Crop DNA Sample

It is estimated that approximately 90% of the corn genome istransposable elements, such as transposons. Because of the repetitivenature of some transposons, phasing alleles is difficult. In order toproduce a corn strain having improved yield and improved nutritionalcontent, a corn double-mutant line is desired. Both mutations aredominant and are found on opposite ends of a chromosome. A high yieldcorn strain is crossed to a high carotenoid level corn strain to produceheterozygous lines, which are then self-crossed to generate segregatingprogeny.

Some of the progeny are observed to demonstrate improved yield andincreased nutritional content. The next step in the project is to crossone of the high yield and high nutritional content strains with a straindemonstrating blight resistance. It is known that the blight resistancemutation loses efficacy if it is contained on the same DNA molecule aseither the high yield mutation or the improved nutritional contentmutation. To minimize timely and costly downstream sequencing andphenotyping experiments, it is desired to perform the blight resistantstrain cross with a parental strain that contains the high yield andhigh nutritional content mutations on the same DNA molecule.

The two parent lines from the initial cross are near-isogenic lines,bred so that variation in their genomes is minimized. As a result, veryfew markers are found available to facilitate phase determination. DNAis extracted from the thousands of resulting seedlings for sequencing todetermine which contain the yield and nutrition mutations in phase onthe same DNA molecule. Because the yield gene and carotenoid gene areseparated by repetitive, highly conserved transposable elements, andbecause there is very little variation between the lines aside fromthese mutations, short read sequencing machines cannot provide phasinginformation. Because the yield gene mutation and the carotenoid genemutation are found at opposite ends of a chromosome, both mutations arenot able to be detected on a single long read by long-read sequencingtechnology. As a result, it is not known whether any of the thousands ofseedlings possess the desired combination of the high yield mutation andthe high nutrition mutation in phase on a single chromosome. It isdetermined the project cannot remain within budget and therefore theproject is cancelled.

Example 4. Successful Phasing of Transposon-Rich Crop DNA Sample

DNA samples from the corn seedlings of Example 3 are extracted andmodified to generate segment-shuffled phase preserved sequencinglibraries. The resulting rearranged DNA molecules are sequenced on along-read sequencing machine. Single sequence reads are obtainedspanning the yield mutation locus and the nutrition mutation locus,separated by one or more punctuation oligonucleotides. Reads indicatingthat the two beneficial mutations are in phase on a single molecule areobserved for some of the seedling samples. One of the confirmed in-phasehigh yield and improved nutritional content strains is selected andcrossed with the blight resistant strain in order to produce a robustcorn strain that will yield much needed increased nutrition indeveloping countries.

This example demonstrates how the methods and compositions disclosedherein are used to determine phase information for complex genomeshaving multiple repetitive elements. This technology allows accurate,rapid phase determination even in complex genomes such as those ofrelevant crop species.

Example 5. Mutation-Baring Nucleic Acid with Indistinguishable Phase

A diploid organism contains two copies of each chromosome of geneticmaterial. Two mutations separated by at least 30 kb of identicalsequence are present on a single chromosome of the diploid genome. TheDNA sample is sequenced on a long-read sequencing machine having anaverage read length of 15 kb. It is impossible to determine if the twomutations are contained on the same or different nucleic acid molecules.

Example 6. Determining Phase Information of a Nucleic Acid Sample

DNA is extracted from the organism of Example 5. DNA is assembled invitro with DNA-binding proteins to generate reconstituted chromatin. Thereconstituted chromatin is cleaved to produce sticky ends, which arepartially filled in to prevent re-ligation. Punctuation oligonucleotideswith ends compatible with the partially filled in sticky ends are addedto the chromatin sample along with a DNA ligase. In some instances, thepunctuation oligonucleotides are dephosphorylated in order to avoidcontatemerization of the oligonucleotides. The DNA segments of there-ligated chromatin sample are rearranged compared to the starting DNAsample, though phase information is maintained since the molecule isbound to chromatin proteins through the punctuation process. In someinstances, the two mutations within the genome are rearranged such thatthey are less than 15 kb apart. In this case, the separation distance isless than that of the average read length of a long-read sequencingmachine. When the rearranged DNA sample is released from the chromatinproteins and sequenced, phase information is determined and sequenceinformation is generated sufficient to generate a de novo sequencescaffold.

Example 7. Determining Phase Information of a Nucleic Acid Sample—BluntLigation

DNA is extracted from the organism of Example 5 and reassembled withDNA-binding proteins in vitro to generate reconstituted chromatin. DNAis cleaved to produce blunt ends. Punctuation oligonucleotides havingblunt ends are ligated to the blunt ends of the cleaved DNA sample. Thepunctuation oligonucleotides are dephosphorylated in order to avoidcontatemerization of the oligonucleotides. The rearranged DNA sample isreleased from the chromatin proteins and sequenced as in Example 6. Whenthe rearranged DNA sample is released from the chromatin proteins andsequenced, phase information is determined and sequence information isgenerated sufficient to generate a de novo sequence scaffold.

Example 8. Barcoding a Punctuation Molecule—Short Read

A DNA sample comprising punctuation oligonucleotides is generated asdescribed in any of Examples 6-7. Following release from DNA-bindingproteins, the free DNA sample, referred to as a punctuated DNA molecule,is contacted to oligonucleotides comprising at least two segments. Onesegment contains a barcode and a second segment contains a sequencecomplementary to the punctuation sequence. After annealing to thepunctuation sequences, the barcoded oligonucleotides are extended withpolymerase to yield barcoded molecules from the same DNA molecule. Thesebarcoded molecules comprise a barcode sequence, the punctuationcomplementary sequence, and genomic sequence. Extension products aresequenced on a short-read sequencing machine and phase information isdetermined by grouping sequence reads having the same barcode into acommon phase.

Example 9. Barcoding a Punctuation Molecule—Long Read

A DNA sample is extracted, punctuated, and barcoded as in Example 8.Following extension, barcoded products are bulk ligated together togenerate long molecules which are read using long-read sequencingtechnology. The embedded read pairs are identifiable via theamplification adapters and punctuation sequences. Further phaseinformation is obtained from the barcode sequence of the read pair.

Example 10. Determining Phase Information with Transposon Punctuations

The DNA sample of Example 5 is extracted and reassembled withDNA-binding proteins in vitro to generate reconstituted chromatin.Transposase bound to two unlinked punctuation oligonucleotides is addedto the DNA sample. The transposase cleaves exposed DNA segments andinserts the two punctuation oligonucleotides into the DNA. Because thepunctuation oligonucleotides in a given transposase are unlinked, theinsertion results in two free DNA ends, each terminated by one of thetwo punctuation oligonucleotides and each tethered to the reconstitutedchromatin to preserve phase information. DNA ligase is added to thesample to ligate blunt DNA ends together, resulting in a rearrangementof DNA segments, though phase information is maintained since the DNAmolecule is bound to the chromatin proteins throughout this process. Therearranged DNA sample is released from the chromatin proteins andsequenced as in Example 6 to determine phase information.

Example 11. Determining Phase Information with TransposonPunctuations—Short Reads

A DNA sample is extracted, reassembled in vitro into reconstitutedchromatin, and punctuated with transposases as described in Example 10.Following re-ligation of blunt ends, re-ligated DNA segments arereleased from protein-DNA complex by restriction digestion, resulting ina plurality of paired ends, which are subsequently ligated toamplification adapters. Following amplification, paired ends aresequenced with short reach technology. It is confidently concluded thatfor either side of a punctuated junction, the punctuation-adjacentsequence is derived from a common phase of a common molecule.

Example 12. Determining Phase Information with TransposonPunctuations—Long Reads

A DNA sample is extracted, reassembled in vitro into reconstitutedchromatin, and punctuated with transposases as described in Example 10.Following re-ligation of blunt ends, re-ligated DNA segments arereleased from protein-DNA complex by restriction digestion, resulting ina plurality of paired ends, which are subsequently ligated toamplification adapters. Following amplification, the plurality of pairedends is bulk ligated together to generate long molecules which are readusing long-read sequencing technology. The embedded read pairs areidentifiable via the native DNA sequence adjacent to the transposasepunctuation sequences. The concatenated punctuated junctions are read ona long-sequence device, and sequence information for multiple junctionsis obtained. Junctions are found to map to multiple differentchromosomes. However, it is confidently concluded that for either sideof a punctuated junction, the punctuation-adjacent sequence is derivedfrom a common phase of a common molecule.

Example 13. Concatemer Generation of Chicago Pairs

A DNA sample is extracted, and assembled with DNA-binding proteins invitro to generate reconstituted chromatin. DNA is cleaved to producesticky ends. The sticky ends are filled in with biotinylated nucleotidesfollowed by blunt ligation of the filled-in ends to generate DNA segmentpairs, referred to as Chicago pairs. These reshuffled nucleic acids arereleased from the chromatin proteins, cleaved and streptavidin-bindingligation junctions are isolated. Amplification adapters are added to thefree ends of the Chicago pairs. Following amplification, Chicago pairsare bulk ligated together to generate long molecules which are readusing a long-read sequencing technology. The embedded read pairs areidentifiable via the amplification adapters. Sequence repeats generatedin the ‘fill-in process’ used to introduce the biotinylated bases arealso used to identify junctions connecting in phase sequence.

The ligated concatemers are sequenced in a single read of a long-readsequencing device. Because the individual junctions are concatenated,one is able to sequence multiple junctions in a single read.

Example 14. Phasing Hairpin DNA Molecule

A long, punctuated DNA molecule, as generated in any of Examples 6, 7,9, 10, or 12, is ligated on one end to a hairpin adapter, resulting in aself-annealing single-stranded molecule harboring an inverted repeat.The molecule is fed through a sequencing enzyme and full length sequenceof each side of the inverted repeat is obtained. The resulting sequenceread corresponds to 2× coverage of a punctuated DNA molecule harboringmultiple rearranged segments, each conveying phase information.Sufficient sequence is generated to independently generate a de novoscaffold of the nucleic acid sample.

Example 15. Phasing a Circularized DNA Molecule

A long, punctuated DNA molecule, as generated in any of Examples 6, 7,9, 10, or 12, is cleaved to form a population of double strandedmolecules of a desired length. These molecules are ligated on each endto single stranded adapters. The result is a double stranded DNAtemplate capped by hairpin loops at both ends. The circular moleculesare sequenced by continuous sequencing technology. Continuous long readsequencing of molecules containing a long double stranded segmentresults in a single contiguous read of each molecule. Continuoussequencing of molecules containing a short double stranded segmentresults in multiple reads of the molecule, which are used either aloneor along with continuous long read sequence information to confirm aconsensus sequence of the molecule. Genomic segment borders marked bypunctuation oligos are identified, and it is concluded that sequenceadjacent to a punctuation border is in phase. Sufficient sequence isgenerated to independently generate a de novo scaffold of the nucleicacid sample.

Example 16. Phased Sequence Assembly Using Multiple Punctuated DNAMolecules

A plurality of punctuated DNA molecules is generated as described in anyof Examples 6, 7, 9, 10, or 12, and subsequently sequenced usinglong-read sequencing technology. Sequences from the plurality ofpunctuated DNA molecules are compared. It is observed that two moleculesof the plurality share sequence in common, but have been independentlyderived and have different punctuation oligos. For a given punctuationoligo on the first molecule, sequence is determined on either side ofeach of the punctuation oligos, and it is concluded that the sequencesegments on either side of the punctuation oligos are in phase on acommon molecule. However, the relative positions of the in-phasesegments are not clear.

One segment of the first punctuated DNS molecule is compared to thesequence of the second punctuated DNA molecule. It is found that asegment end near a punctuation oligo of the first molecule maps to theinterior of a segment of the second punctuated DNA molecule. Sequence ofthe segment of the second punctuated oligo that aligns beyond thepunctuation oligo of the first punctuated DNA molecule is mapped to thefirst punctuation DNA molecule and a distal segment is identified. Usingthe second DNA molecule segment as a guide, it is determined that twosegments of the first punctuated DNA molecule were positioned adjacentto one another in the original nucleic acid sample.

That is, the first punctuated molecule is used to determine phaseinformation for its constituent segments, while comparison tounpunctuated regions of the second (and additional) punctuated DNAmolecules is used to order the segments of the first punctuatedmolecule. Repeating this process reciprocally, phase and orderinformation is determined for the majority of the segments in each ofthe plurality of punctuation oligos.

The resulting assembled sequence is a phased sequence of the input DNAmolecule prior to rearrangement occurring, and represents a de novo,phased assembly of the nucleic acid sample.

Example 17. Phasing Short-Read Sequencing Data with Long-Read SequenceData

A punctuated DNA molecule is generated as described in any of Examples6, 7, 9, 10, or 12 and subsequently sequenced using long-read sequencingtechnology. In parallel, the input DNA is sequenced using standardshort-read shotgun sequencing technology. The shotgun sequence from thesample is mapped to the long-read data generated from the rearranged DNAmolecule. The phased genomic sequence reads from the punctuated moleculeare mapped to sequencing data obtained from the concurrently generatedshort-read sequencing. Some of the short-reads map to the long-readgenerated sequence. This overlap allows short sequence reads to beassigned to the same phase as the genomic sequence generated from thepunctuated DNA molecule long sequence read.

Example 18. Nucleic Acid Sequence Library—Long Reads

A plurality of punctuated DNA molecules is generated as described in anyof Examples 6, 7, 9, 10, or 12, and subsequently sequenced usinglong-read sequencing technology. Each punctuated molecule is sequenced,and the sequence reads are analyzed. Sequence reads average 10 kb forthe sequence reaction. Sequence reads are identified that comprise atleast 500 bases of a first segment and 500 bases of a second segment,joined by a punctuation oligo sequence. The first and second segmentsequences are mapped to a scaffold genome and are found to map tocontigs that are separated by at least 100 kb.

The first contig and the second contig each comprise a singleheterozygous position, the phase of which is not determined in thescaffold. The heterozygous position of the first contig is spanned bythe first segment of the long read, and the heterozygous position of thesecond contig is spanned by the 500 bases of the second segment of thelong read.

The reads each span their contigs' respective heterozygous regions.Sequence of the read segments indicates that a first allele of the firstcontig and a first allele of the second contig are in phase. Sincesequences from the first and second nucleic acid segments are detectedin a single long sequence read, it is determined that the first andsecond nucleic acid segments are comprised on the same DNA molecule inthe input DNA sample.

This example demonstrates that long reads from punctuation moleculesprovide phase information for contigs that are positioned far apart fromone another on a genome scaffold. The example also demonstrates that themapping is done with a high degree of confidence because the size ofeach segment adjacent to the punctuation oligo is great enough tofacilitate accurate mapping, and increases the likelihood that aheterozygous position is spanned.

Example 19. Nucleic Acid Sequence Library—Short Reads

A plurality of paired end molecules is generated as described in eitherExample 8 or 11, and subsequently sequenced using long read sequencingtechnology. The average read length for the library is determined to be1 kb. Paired end molecules comprise a first DNA segment and a second DNAsegment that, within the input DNA sample, are in phase and separated bya distance greater than 10 kb. Sequence reads are generated from pairedend molecules, some of which comprise at least 300 bases of sequencefrom a first nucleic acid segment and at least 300 bases of sequencefrom a second nucleic acid segment. Since sequences from the first andsecond nucleic acid segments are detected in a single sequence read, itis determined that the first and second nucleic acid segments are inphase on the same DNA molecule in the input DNA sample.

This example illustrates that using the rearranged punctuated moleculesas taught herein, one generates sequence libraries that yield phaseinformation for DNA segments that are separated in the nucleic acidsample by greater than the read length of the sequencing technology usedto sequence them.

Example 20. Nucleic Acid Sequence Library—Concurrent Phased DNA Assembly

A plurality of sequence reads is generated from a punctuated DNAlibrary. The library conveys phase information as described in eitherExample 18 or 19, such that segments on either side of a punctuationevent are determined to be in phase on a single molecule. In addition,the generated sequence reads represents at least 80% of the nucleic acidsequence of the input DNA sample. The sequence reads are used togenerate de novo contig information that spans at least 80% of the inputDNA sample. Additionally, the sequence reads are used to determine phaseinformation, which is subsequently used to order and orient the contigsrelative to each other in order to generate a phased sequence assemblyof the input DNA sample.

This example illustrates that punctuated DNA molecules convey phaseinformation and also in some cases encompass sequence informationcomprising a substantial portion of the total nucleic acid sequence,such that a de novo sequence assembly is concurrently generated.

Example 21. DNA Molecule Phasing

A high molecular weight (HMW) DNA sample is extracted which comprises atleast some DNA molecules of at least 100 kb in length. One of the 100 kbDNA molecules comprises a first DNA segment and a second DNA segmentthat are separated by distance that is greater than the average readlength of standard sequencing technologies. The nucleic acid sample isdiploid but comprises large regions of sequence identity, complicatingphase determination.

For confident phase determination, the first and second DNA segmentsneed to be detected within a single sequencing read. Therefore, therelative position of the first and second DNA segments must be changedsuch that the first and second DNA segments are separated by a distancethat is less than the average read length of standard sequencingtechnologies. This rearrangement must not result in loss of phaseinformation. This rearrangement is achieved by the methods disclosedherein and as described within any of Examples 6, 7, or 10. Duringphase-maintaining rearrangement, no more than 10% of the starting HMWDNA molecule is deleted. That is, the first segment and the secondsegment are not brought into proximity simply by deleting theintervening sequence. Rather, the segments are rearranged relative toone another without deletion of the majority of the interveningsequence. Since nearly the entire input DNA molecule is preserved,following sequencing, the generated sequence reads are used to assemble,order, and orient de novo generated contigs such that nearly the entireinput DNA molecule is sequenced, assembled, and phased.

Example 22. Analysis of Mammalian Cell Culture

A sample of mammalian cell culture is analyzed using the techniquesdescribed herein. Briefly, a cell culture of mammalian cells is grown.The cells are cross-linked, cross-linking is quenched, and the cellpellet is stored at −20° C. Cells are homogenized and nuclei arerecovered in lysis buffer. Nuclei in the homogenate are bound to SPRIbeads and digested using DpnII restriction enzyme. Ends are filled inwith no biotin-11-dCTP and blunt ends are ligated. Cross-linking isreversed, DNA is recovered and cleaned up and prepared for sequencing.Sequencing is conducted with Pacific Biosciences SMRT long-readsequencing. In some cases, the DNA can be size selected for molecules atleast about 6 kb in length prior to sequencing.

Two samples are tested to ensure ligation occurred properly. FIG. 7 isrepresentative of results indicative of a successful ligation inseparate samples. One sees for each sample that ligation has led to ashift toward substantially higher molecular weight nucleic acids.

At FIG. 8, one sees an outcome of such a library generation process. Ofover 1,000,000 circular consensus sequence (CSS) reads, only 300,000 areunmapped. There are 1,500,000 mapped segments (−q 1) and 1,350,000mapped segments (−q 20). For reads with 1 mapped segment, n=500,000; forreads with 2 mapped segments, n=175,000; for reads with 3 mappedsegments, n=75,000; for reads with 4 mapped segments, n=30,000; forreads for 5 mapped segments, n=15,000; for reads with 6 mapped segments,n=7,000. This demonstrates that segments are readily identified, andthat sequencing the library generation protocol generates reads spanningmultiple rearranged segments

Table 1 shows clone coverage from reads having the indicated number ofmapping segments. As indicated therein, the library generation protocolyields substantial whole genome coverage in total segment sequence,while yielding valuable phasing information as indicated by the numberof clones having two or more mapping segments. As many genomes haverepetitive sequence, the number of uniquely mapped segments is anunderestimate of the total number of segments in a rearranged libraryconstituent molecule.

TABLE 1 Approximate clone coverage from reads with X maximum number ofmapping segments. # mapped segments 1 2 3 4 5 6 base pairs1,3000,000,000 18,000,000,000 9,000,000,000 4,000,000,000 1,500,000,000500,000,000 Fold genome 0.4 X 6 X 3 X 1.2 X 0.5 X 0.5 X (3. Gb)

At FIGS. 9A-9B one sees frequency distributions of distance spanned byreads with X mapped segments for a sample, sorted into 10 kb bins (FIG.9A) and 1 kb bins (FIG. 9B). Data in this figure reaffirms theconclusion that library generation protocols as disclosed herein yieldreads having multiple uniquely mapping segments ligated at recognizablejunctions, so as to provide both genome sequence information (oftencomprising polymorphisms) and phase information, so that thesepolymorphisms can be phased relative to one another even if they occurin a sample genome at distances greater than the length of a sequenceread and are separated by sequence that does not have markers ofheterozygosity.

1.-44. (canceled)
 45. A method of sequencing a first DNA molecule,comprising: (a) providing a first DNA molecule having a first segment, asecond segment, and a third segment, wherein the first segment and thesecond segment are not adjacent on the first DNA molecule, and whereinthe third segment is not adjacent to the first segment or the secondsegment on the first DNA molecule; (b) contacting the first DNA moleculeto a DNA binding moiety such that the first segment, the second segment,and the third segment are held together independent of a commonphosphodiester backbone of the first DNA molecule; (c) cleaving thefirst DNA molecule such that the first segment, the second segment, andthe third segment are not joined by a common phosphodiester backbone andcomprise at least one exposed end; (d) attaching the first segment tothe second segment via a phosphodiester bond and attaching the thirdsegment to the second segment via a phosphodiester bond to form areassembled first DNA molecule; and (e) sequencing at least a portion ofthe reassembled first DNA molecule comprising a junction between thefirst segment and the second segment and a junction between the secondsegment and the third segment in a single sequencing read.
 46. Themethod of claim 45, wherein the DNA binding moiety comprises a pluralityof DNA-binding molecules.
 47. The method of claim 46, wherein contactingthe first DNA molecule to a plurality of DNA-binding molecules comprisescontacting to a population of DNA-binding proteins.
 48. The method ofclaim 46, wherein contacting the first DNA molecule to a plurality ofDNA-binding moieties comprises contacting to a population of DNA-bindingnanoparticles.
 49. The method of claim 46, wherein contacting the firstDNA molecule to a plurality of DNA-binding moieties comprises contactingthe first DNA molecule to a cross-linking agent.
 50. The method of claim45, wherein cleaving the first DNA molecule comprises contacting to arestriction endonuclease.
 51. The method of claim 45, wherein cleavingthe first DNA molecule comprises contacting to a nonspecificendonuclease.
 52. The method of claim 45, wherein cleaving the first DNAmolecule comprises contacting to a tagmentation enzyme.
 53. The methodof claim 45, wherein cleaving the first DNA molecule comprisescontacting to a transposase.
 54. The method of claim 45, whereincleaving the first DNA molecule comprises shearing the first molecule.55. The method of claim 45, comprising adding a tag to at least oneexposed end of the first segment, the second segment, or the thirdsegment.
 56. The method of claim 55, wherein the tag comprises at leastone tag selected from the list consisting of a labeled base, amethylated base, a biotinylated base, uridine, and a noncanonical base.57. The method of claim 45, wherein the first segment comprises a firstsegment sticky end, the method further comprising adding a linker oligocomprising an overhang that anneals to the first segment sticky end. 58.The method of claim 45, wherein attaching comprises a method selectedfrom the group consisting of ligating and DNA single strand nick repair.59. The method of claim 45, wherein the first segment and the secondsegment are separated by at least 10 kb on the first DNA molecule priorto cleaving the first DNA molecule.
 60. The method of claim 45, whereinthe sequencing comprises single molecule long-read sequencing.
 61. Themethod of claim 60, wherein the long-read sequencing comprises a read ofat least 5 kb.
 62. The method of claim 45, wherein the first reassembledfirst DNA molecule comprises a hairpin moiety linking a 5′ end to a 3′end at one end of the first DNA molecule.
 63. The method of claim 45,comprising sequencing a second reassembled version of the first DNAmolecule.
 64. The method of claim 45, wherein first segment sequence,second segment sequence, and third segment sequence representlong-distance phase information from the first DNA molecule.